Insights from the predicted epitope similarity between Mycobacterium tuberculosis virulent factors and its human homologs

Unveiling the ESR1 Conformational Stability and Screening Potent Inhibitors for Breast Cancer Treatment

BACKGROUND

The current study recognizes the significance of estrogen receptor alpha (ERα) as a member of the nuclear receptor protein family, which holds a central role in the pathophysiology of breast cancer. ERα serves as a valuable prognostic marker, with its established relevance in predicting disease outcomes and treatment responses.

METHODS

In this study, computational methods are utilized to search for suitable drug-like compounds that demonstrate analogous ligand binding kinetics to ERα.

RESULTS

Docking-based simulation screened out the top 5 compounds - ZINC13377936, NCI35753, ZINC35465238, ZINC14726791, and NCI663569 against the targeted protein. Further, their dynamics studies reveal that the compounds ZINC13377936 and NCI35753 exhibit the highest binding stability and affinity.

CONCLUSION

Anticipating the competitive inhibition of ERα protein expression in breast cancer, we envision that both ZINC13377936 and NCI35753 compounds hold substantial promise as potential therapeutic agents. These candidates warrant thorough consideration for rigorous In vitro and In vivo evaluations within the context of clinical trials. The findings from this current investigation carry significant implications for the advancement of future diagnostic and therapeutic approaches for breast cancer.

Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation of EGFR for the Clinical Treatment of Glioblastoma

Glioblastoma (GBM) is a WHO Grade IV tumor with poor visibility, a high risk of comorbidity, and exhibit limited treatment options. Resurfacing from second-rate glioma was originally classified as either mandatory or optional. Recent interest in personalized medicine has motivated research toward biomarker stratification-based individualized illness therapy. GBM biomarkers have been investigated for their potential utility in prognostic stratification, driving the development of targeted therapy and customizing therapeutic treatment. Due to the availability of a specific EGFRvIII mutational variation with a clear function in glioma-genesis, recent research suggests that EGFR has the potential to be a prognostic factor in GBM, while others have shown no clinical link between EGFR and survival. The pre-existing pharmaceutical lapatinib (PubChem ID: 208,908) with a higher affinity score is used for virtual screening. As a result, the current study revealed a newly screened chemical (PubChem CID: 59,671,768) with a higher affinity than the previously known molecule. When the two compounds are compared, the former has the lowest re-rank score. The time-resolved features of a virtually screened chemical and an established compound were investigated using molecular dynamics simulation. Both compounds are equivalent, according to the ADMET study. This report implies that the virtual screened chemical could be a promising Glioblastoma therapy.

Comparative Reverse Vaccinology of Piscirickettsia salmonis, Aeromonas salmonicida, Yersinia ruckeri, Vibrio anguillarum and Moritella viscosa, Frequent Pathogens of Atlantic Salmon and Lumpfish Aquaculture

Marine finfish aquaculture is affected by diverse infectious diseases, and they commonly occur as co-infection. Some of the most frequent and prevalent Gram-negative bacterial pathogens of the finfish aquaculture include Piscirickettsia salmonis, Aeromonas salmonicida, Yersinia ruckeri, Vibrio anguillarum and Moritella viscosa. To prevent co-infections in aquaculture, polyvalent or universal vaccines would be ideal. Commercial polyvalent vaccines against some of these pathogens are based on whole inactivated microbes and their efficacy is controversial. Identification of common antigens can contribute to the development of effective universal or polyvalent vaccines. In this study, we identified common and unique antigens of P. salmonis, A. salmonicida, Y. ruckeri, V. anguillarum and M. viscosa based on a reverse vaccinology pipeline. We screened the proteome of several strains using complete available genomes and identified a total of 154 potential antigens, 74 of these identified antigens corresponded to secreted proteins, and 80 corresponded to exposed outer membrane proteins (OMPs). Further analysis revealed the outer membrane antigens TonB-dependent siderophore receptor, OMP assembly factor BamA, the LPS assembly protein LptD and secreted antigens flagellar hook assembly protein FlgD and flagellar basal body rod protein FlgG are present in all pathogens used in this study. Sequence and structural alignment of these antigens showed relatively low percentage sequence identity but good structural homology. Common domains harboring several B-cells and T-cell epitopes binding to major histocompatibility (MHC) class I and II were identified. Selected peptides were evaluated for docking with Atlantic salmon (Salmo salar) and Lumpfish MHC class II. Interaction of common peptide-MHC class II showed good in-silico binding affinities and dissociation constants between −10.3 to −6.5 kcal mol−1 and 5.10 × 10−9 to 9.4 × 10−6 M. This study provided the first list of antigens that can be used for the development of polyvalent or universal vaccines against these Gram-negative bacterial pathogens affecting finfish aquaculture.

Experimental and Computational Approaches to Improve Binding Affinity in Chemical Biology and Drug Discovery

Drug discovery is one of the most complicated processes and establishment of a single drug may require multidisciplinary attempts to design efficient and commercially viable drugs. The main purpose of drug design is to identify a chemical compound or inhibitor that can bind to an active site of a specific cavity on a target protein. The traditional drug design methods involved various experimental based approaches including random screening of chemicals found in nature or can be synthesized directly in chemical laboratories. Except for the long cycle design and time, high cost is also the major issue of concern. Modernized computer-based algorithm including structure-based drug design has accelerated the drug design and discovery process adequately. Surprisingly from the past decade remarkable progress has been made concerned with all area of drug design and discovery. CADD (Computer Aided Drug Designing) based tools shorten the conventional cycle size and also generate chemically more stable and worthy compounds and hence reduce the drug discovery cost. This special edition of editorial comprises the combination of seven research and review articles set emphasis especially on the computational approaches along with the experimental approaches using a chemical synthesizing for the binding affinity in chemical biology and discovery as a salient used in de-novo drug designing. This set of articles exfoliates the role that systems biology and the evaluation of ligand affinity in drug design and discovery for the future.

A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma

BACKGROUND

Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32).

AIM

The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL.

METHODOLOGY

Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds.

RESULT

MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies.

CONCLUSION

Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.

Artificial Intelligence, Big Data and Machine Learning Approaches in Precision Medicine & Drug Discovery

Artificial Intelligence revolutionizes the drug development process that can quickly identify potential biologically active compounds from millions of candidate within a short period. The present review is an overview based on some applications of Machine Learning based tools, such as GOLD, Deep PVP, LIB SVM, etc. and the algorithms involved such as support vector machine (SVM), random forest (RF), decision tree and Artificial Neural Network (ANN), etc. at various stages of drug designing and development. These techniques can be employed in SNP discoveries, drug repurposing, ligand-based drug design (LBDD), Ligand-based Virtual Screening (LBVS) and Structure- based Virtual Screening (SBVS), Lead identification, quantitative structure-activity relationship (QSAR) modeling, and ADMET analysis. It is demonstrated that SVM exhibited better performance in indicating that the classification model will have great applications on human intestinal absorption (HIA) predictions. Successful cases have been reported which demonstrate the efficiency of SVM and RF models in identifying JFD00950 as a novel compound targeting against a colon cancer cell line, DLD-1, by inhibition of FEN1 cytotoxic and cleavage activity. Furthermore, a QSAR model was also used to predict flavonoid inhibitory effects on AR activity as a potent treatment for diabetes mellitus (DM), using ANN. Hence, in the era of big data, ML approaches have been evolved as a powerful and efficient way to deal with the huge amounts of generated data from modern drug discovery to model small-molecule drugs, gene biomarkers and identifying the novel drug targets for various diseases.

Most Promising Compounds for Treating COVID-19 and Recent Trends in Antimicrobial & Antifungal Agents

Multidrug resistance in microbes poses a major health crisis and demands for the discovery of novel antimicrobial agents. The recent pandemic of SARS-CoV-2 has raised a public health emergency in almost all the countries of the world. Unlike viruses, a bacterium plays a significant role in various environmental issues such as bioremediation. Furthermore, biosurfactants produced by various bacterial species have an edge over traditionally produced chemical surfactants for its biodegradability, low toxicity and better interfacial activity with various applications in agriculture and industry. This special issue focuses on the global perspective of drug discovery for various antimicrobial, antiviral, and antifungal agents for infectious diseases. The issue also emphasizes the ongoing developments and the role of microbes in environmental remediation. We wish the articles published in this issue will enhance the current understanding in microbiology among the readers, and serve as the "seed of an idea" for drug development for ongoing COVID-19 pandemic.

Shape-based Machine Learning Models for the Potential Novel COVID-19 Protease Inhibitors Assisted by Molecular Dynamics Simulation

BACKGROUND

The vast geographical expansion of novel coronavirus and an increasing number of COVID-19 affected cases have overwhelmed health and public health services. Artificial Intelligence (AI) and Machine Learning (ML) algorithms have extended their major role in tracking disease patterns, and in identifying possible treatments.

OBJECTIVE

This study aims to identify potential COVID-19 protease inhibitors through shape-based Machine Learning assisted by Molecular Docking and Molecular Dynamics simulations.

METHODS

31 Repurposed compounds have been selected targeting the main coronavirus protease (6LU7) and a machine learning approach was employed to generate shape-based molecules starting from the 3D shape to the pharmacophoric features of their seed compound. Ligand-Receptor Docking was performed with Optimized Potential for Liquid Simulations (OPLS) algorithms to identify highaffinity compounds from the list of selected candidates for 6LU7, which were subjected to Molecular Dynamic Simulations followed by ADMET studies and other analyses.

RESULTS

Shape-based Machine learning reported remdesivir, valrubicin, aprepitant, and fulvestrant as the best therapeutic agents with the highest affinity for the target protein. Among the best shape-based compounds, a novel compound identified was not indexed in any chemical databases (PubChem, Zinc, or ChEMBL). Hence, the novel compound was named 'nCorv-EMBS'. Further, toxicity analysis showed nCorv-EMBS to be suitable for further consideration as the main protease inhibitor in COVID-19.

CONCLUSION

Effective ACE-II, GAK, AAK1, and protease 3C blockers can serve as a novel therapeutic approach to block the binding and attachment of the main COVID-19 protease (PDB ID: 6LU7) to the host cell and thus inhibit the infection at AT2 receptors in the lung. The novel compound nCorv- EMBS herein proposed stands as a promising inhibitor to be evaluated further for COVID-19 treatment.

Immunoinformatics and analysis of antigen distribution of Ureaplasma diversum strains isolated from different Brazilian states

BACKGROUND

Ureaplasma diversum has numerous virulence factors that contribute to pathogenesis in cattle, including Lipid-associated membrane proteins (LAMPs). Therefore, the objectives of this study were to evaluate in silico important characteristics for immunobiological applications and for heterologous expression of 36 LAMPs of U. diversum (UdLAMPs) and, also, to verify by conventional PCR the distribution of these antigens in strains of Brazilian states (Bahia, Minas Gerais, São Paulo, and Mato Grosso do Sul). The Manatee database was used to obtain the gene and peptide sequences of the antigens. Similarity and identity studies were performed using BLASTp and direct antigenicity was evaluated by the VaxiJen v2.0 server. Epitope prediction for B lymphocytes was performed on the BepiPred v2.0 and CBTOPE v1.0 servers. NetBoLApan v1.0 was used to predict CD8⁺ T lymphocyte epitopes. Subcellular location and presence of transmembrane regions were verified by the software PSORTb v3.0.2 and TMHMM v2.2 respectively. SignalP v5.0, SecretomeP v2.0, and DOLOP servers were used to predict the extracellular excretion signal. Physico-chemical properties were evaluated by the web-software ProtParam, Solpro, and Protein-sol.

RESULTS

In silico analysis revealed that many UdLAMPs have desirable properties for immunobiological applications and heterologous expression. The proteins gudiv_61, gudiv_103, gudiv_517, and gudiv_681 were most promising. Strains from the 4 states were PCR positive for antigens predicted with immunogenic and/or with good characteristics for expression in a heterologous system.

CONCLUSION

These works contribute to a better understanding of the immunobiological properties of the UdLAMPs and provide a profile of the distribution of these antigens in different Brazilian states.

Role of Infections in the Pathogenesis of Rheumatoid Arthritis: Focus on Mycobacteria

Rheumatoid arthritis (RA) is a systemic inflammatory autoimmune disease characterized by chronic erosive polyarthritis. A complex interaction between a favorable genetic background, and the presence of a specific immune response against a broad-spectrum of environmental factors seems to play a role in determining susceptibility to RA. Among different pathogens, mycobacteria (including Mycobacterium avium subspecies paratuberculosis, MAP), and Epstein–Barr virus (EBV), have extensively been proposed to promote specific cellular and humoral response in susceptible individuals, by activating pathways linked to RA development. In this review, we discuss the available experimental and clinical evidence on the interplay between mycobacterial and EBV infections, and the development of the immune dysregulation in RA.

Computer-Aided Structure Prediction of Bluetongue Virus Coat Protein VP2 Assisted by Optimized Potential for Liquid Simulations (OPLS)

Background:

The capsid coated protein of Bluetongue virus (BTV) VP2 is responsible for BTV transmission by the Culicoides vector to vertebrate hosts. Besides, VP2 is responsible for BTV entry into permissive cells and hence plays a major role in disease progression. However, its mechanism of action is still unknown.

Objective:

The present investigation aimed to predict the 3D structure of Viral Protein 2 of the bluetongue virus assisted by Optimized Potential for Liquid Simulations (OPLS), structure validation, and an active site prediction.

Methods:

The 3D structure of the VP2 protein was built using a Python-based Computational algorithm. The templates were identified using Smith waterman’s Local alignment. The VP2 protein structure validated using PROCHECK. Molecular Dynamics Simulation (MDS) studies were performed using an academic software Desmond, Schrodinger dynamics, for determining the stability of a model protein. The Ligand-Binding site was predicted by structure comparison using homology search and proteinprotein network analysis to reveal their stability and inhibition mechanism, followed by the active site identification.

Results:

The secondary structure of the VP2 reveals that the protein contains 220 alpha helix atoms, 40 310 helix, 151 beta sheets, 134 coils and 424 turns, whereas the 3D structure of Viral Protein 2 of BTV has been found to have 15774 total atoms in the structure. However, 961 amino acids were found in the final model. The dynamical cross-correlation matrix (DCCM) analysis tool identifies putative protein domains and also confirms the stability of the predicted model and their dynamical behavior difference with the correlative fluctuations in motion.

Conclusion:

The biological interpretation of the Viral Protein 2 was carried out. DCCM maps were calculated, using a different coordinate reference frame, through which, protein domain boundaries and protein domain residue constituents were identified. The obtained model shows good reliability. Moreover, we anticipated that this research should play a promising role in the identification of novel candidates with the target protein to inhibit their functional significance.

In Silico Insights on GD2 : A Potential Target for Pediatric Neuroblastoma

Background:

Originating from the abnormal growth of neuroblasts, pediatric neuroblastoma affects the age group below 15 years. It is an aggressive heterogenous cancer with a high morbidity rate. Biological marker GD2 synthesised by the GD2 gene acts as a powerful predictor of neuroblastoma cells. GD2 gangliosides are sialic acid-containing glycosphingolipids. Differential expression during brain development governs the function of the GD2. The present study explains the interaction of the GD2 with its established inhibitors and discovers the compound having a high binding affinity against the target protein. Technically, during the development of new compounds through docking studies, the best drug among all pre-exist inhibitors was filtered. Hence in reference to the best docked compound, the study proceeded further.

Methodology:

The In silico approach provides a platform to determine and establish potential inhibitor against GD2 in Pediatric neuroblastoma. The 3D structure of GD2 protein was modelled by homology base fold methods using Smith-Watermans’ Local alignment. A total of 18 established potent compounds were subjected to molecular docking and Etoposide (CID: 36462) manifested the highest affinity. The similarity search presented 336 compounds similar to Etoposide.

Results:

Through virtual screening, the compound having PubChem ID 10254934 showed a better affinity towards GD2 than the established inhibitor. The comparative profiling of the two compounds based on various interactions such as H-bond interaction, aromatic interactions, electrostatic interactions and ADMET profiling and toxicity studies were performed using various computational tools.

Conclusion:

The docking separated the virtual screened drug (PubChemID: 10254934) from the established inhibitor with a better re-rank score of -136.33. The toxicity profile of the virtual screened drug was also lesser (less lethal) than the established drug. The virtual screened drug was observed to be bioavailable as it does not cross the blood-brain barrier. Conclusively, the virtual screened compound obtained in the present investigation is better than the established inhibitor and can be further augmented by In vitro analysis, pharmacodynamics and pharmacokinetic studies.

Identification of Potent VEGF Inhibitors for the Clinical Treatment of Glioblastoma, A Virtual Screening Approach

Vascular endothelial growth factor (VEGF) expression could be found in all glioblastomas. VEGF takes part in numerous changes including the endothelial cell proliferation, the vasculature of solid tumor: its survival invasion, and migration, chemotaxis of bone marrow-derived progenitor cells, vasodilation and vascular permeability. VEGF inhibition can be a smart therapeutic strategy because it is extremely specific and less toxic than cytotoxic therapy. To establish better inhibition of VEGF than the current inhibitors, present study approach is by molecular docking, virtual screening to illustrate the inhibitor with superior affinity against VEGF to have a cautious pharma profile. To retrieve the best established and high-affinity high affinity molecule, Molegro Virtual Docker software was executed. The high-affinity scoring compounds were subjected to further similarity search to retrieve the drugs with similar properties from pubchem database. The completion of virtual screening reveals that PubChem compound SCHEMBL1250485 (PubChem CID: 66965667) has the highest affinity. The study of the drug-likeness was verified using OSIRIS Property Explorer software which supported the virtual screened result. Further ADMET study and drug comparative study strongly prove the superiority of the new established inhibitor with lesser rerank score and toxicity. Overall, the new inhibitor has higher potential to stop the expression of VEGF in glioblastoma and positively can be further analysed through In vitro studies.

Identification of High-affinity Small Molecules Targeting Gamma Secretase for the Treatment of Alzheimer’s Disease

Background:

Alzheimers Disease (AD) is a neurodegenerative disease which is characterized by the deposition of amyloid plaques in the brain- a concept supported by most of the researchers worldwide. The main component of the plaques being amyloid-beta (Aβ42) results from the sequential cleavage of Amyloid precursor protein (APP) by beta and gamma secretase. This present study intends to inhibit the formation of amyloid plaques by blocking the action of gamma secretase protein with Inhibitors (GSI).

Methods:

A number of Gamma Secretase Inhibitors (GSI) were targeted to the protein by molecular docking. The inhibitor having the best affinity was used as a subject for further virtual screening methods to obtain similar compounds. The generated compounds were docked again at the same docking site on the protein to find a compound with higher affinity to inhibit the protein. The highlights of virtually screened compound consisted of Pharmacophore Mapping of the docking site. These steps were followed by comparative assessments for both the compounds, obtained from the two aforesaid docking studies, which included interaction energy descriptors, ADMET profiling and PreADMET evaluations.

Results:

111 GSI classified as azepines, sulfonamides and peptide isosteres were used in the study. By molecular docking an amorpholino-amide, compound (22), was identified to be the high affinity compound GSI along with its better interaction profiles.The virtually screened pubchem compound AKOS001083915 (CID:24462213) shows the best affinity with gamma secretase. Collective Pharmacophore mapping (H bonds, electrostatic profile, binding pattern and solvent accesibility) shows a stable interaction. The resulting ADMETand Descriptor values were nearly equivalent.

Conclusion:

These compounds identified herein hold a potential as Gamma Secretase inhibitors.According to PreADMET values the compound AKOS001083915 is effective and specific to the target protein. Its BOILED-egg plot analysis infers the compound permeable to blood brain barrier.Comparative study for both the compounds resulted in having nearly equivalent properties. These compounds have the capacity to inhibit the protein which is indirectly responsible for the formation of amyloid plaques and can be further put to in vitro pharmacokinetic and dynamic studies.

A Computer - Aided Drug Designing for Pharmacological Inhibition of Mutant ALK for the Treatment of Non-small Cell Lung Cancer

Background:

Lung cancer is the most common among all the types of cancer worldwide with 1.8 million people diagnosed every year, leading to 1.6 million deaths every year according to the American cancer society. The involvement of mutated Anaplasic Lymphoma Kinase (ALK) positive fusion protein in the progression of NSCLC has made a propitious target to inhibit and treat NSCLC. In the present study, the main motif is to screen the most effective inhibitor against ALK protein with the potential pharmacological profile. The ligands selected were docked with Molegro Virtual Docker (MVD) and CEP-37440 (PubChem CID- 71721648) was the best docked pre-established compound with a permissible pharmacological profile.

Methods:

The selected ligands were docked with Molegro Virtual Docker (MVD). With reference to the obtained compound with the lowest re-rank score, PubChem database was virtually screened to retrieve a large set of similar compounds which were docked to find the compound with higher affinity. Further comparative studies and in silico prediction included pharmacophore studies, proximity energy parameters, ADMET and BOILED-egg plot analysis.

Results:

CEP-37440 (PubChem CID- 71721648) was the best docked pre-established compound with preferable pharmacological profile and PubChem compound CID-123449015 came out as the most efficient virtually screened inhibitor. Interestingly, the contours of the virtual screened compound PubChem CID- 123449015 fall within our desired high volume cavity of protein having admirable property to control the ALK regulation to prevent carcinogenesis in NSCLC. BOILED-Egg plot analysis depicts that both the compounds have analogous characteristics in the divergent aspects. Moreover, in the evaluations of Blood Brain Barrier, Human Intestinal Absorption, AMES toxicity, and LD50, the virtually screened compound (PubChem CID-123449015) was found within high optimization.

Conclusion:

These investigations denote that the virtually screened compound (PubChem CID- 123449015) is more efficient to be a better prospective candidate for NSCLC treatment having good pharmacological profile than the pre-established compound CEP-37440 (PubChem CID- 71721648) with low re-rank score. The identified virtually screened compound has high potential to act as an ALK inhibitor and can show promising results in the research of non-small cell lung cancer (NSCLC).

Design of PD-L1 inhibitors for lung cancer

The progression of lung cancer is associated with inactivation of programmed cell death protein 1, abbreviated as PD- 1 which regulates the suppression of the body's immune system by suppressing T- cell inflammatory activity and is responsible for preventing cancer cell growth. It is of interest to identify inhibitors for PD-L1 dimeric structure through molecular docking and virtual screening. The virtual screened compound XGIQBUNWFCCMAS-UHFFFAOYSA-N (PubChem CID: 127263272) displays a high affinity with the target protein. ADMET analysis and cytotoxicity studies further add weight to this compound as a potential inhibitor of PD-L1. The established compound BMS-202 still shows the high re-rank score, but the virtual screened drug possesses a better ADMET profile with a higher intestinal absorption value and lower toxicity.

Design of novel JAK3 Inhibitors towards Rheumatoid Arthritis using molecular docking analysis

Multiple cytokines play a pivotal role in the pathogenesis of Rheumatoid Arthritis by inducing intracellular signaling and it is known that the members of the Janus kinase (JAK) family are essential for such signal transduction. Janus kinase 3 is a tyrosine kinase that belongs to the Janus family of kinases. Drugs targeting JAK3 in the treatment of Rheumatoid arthritis is relevant. Therefore, it is of interest to design suitable inhibitors for JAK3 dimer using molecular docking with Molegro Virtual Docker. The compound possessing the highest affinity score is subjected to virtual screening to retrieve inhibitors. The compound SCHEMBL19100243 (PubChem CID- 76749591) displays a high affinity with the target protein. The affinity scores of this compound are more than known drugs. ADMET analysis and BOILED Egg plot provide insights into this compound as a potent inhibitor of JAK3.

FLT3 inhibitor design using molecular docking based virtual screening for acute myeloid leukemia

Acute Myeloid Leukaemia (AML) is a blood cancer, which affects the red blood cells in the bone marrow. Of the possible proteins that are affected in AML, fms-like tyrosine kinase 3 (FLT3) has long been recognized as a potential therapeutic target as it affects the other signaling pathways and leads to a cascade of events. First-generation inhibitors sorafenib and midostaurin, as well as secondgeneration agents such as quizartinib and crenolanib are known. It is of interest to identify new compounds against FLT3 with improved activity using molecular docking and virtual screening. Molecular docking of existing inhibitors selected a top scoring bestestablished candidate Quizartinib having PubChem CID: 24889392. Similarity searching resulted in compound XGIQBUNWFCCMASUHFFFAOYSA-NPubChemCID: 44598530 which shows higher affinity scores. A comparative study of both the compounds using a drug-drug comparison, ADMET studies, boiled egg plot and pharmacophore parameters and properties confirmed the result and predicted the ligand to be an efficient inhibitor of FLT3.

Virtual Screening of IL-6 Inhibitors for Idiopathic Arthritis

Juvenile idiopathic arthritis (JIA) is a heterogeneous disease characterized by the arthritis of unknown origin and IL6 is a known target for JIA. 20 known inhibitors towards IL-6 were screened and Methotrexate (MTX) having PubChem ID: 126941 showed high binding capacity with the receptor IL-6. The similarity searching with this compound gave 269 virtual screened compounds. The said screening presented 269 possible drugs having structural similarity to Methotrexate. The docking studies of the screened drugs separated the compound having PubChem CID: 122677576 (re-rank value of -140.262). Toxicity and interaction profile validated this compound for having a better affinity with the target protein. Conclusively, this study shows that according to ADMET profile and BOILED-Egg plot, the compound (PubChem CID: 122677576) obtained from Virtual Screen could be the best drug in future during the prevention of juvenile idiopathic arthritis. In the current study, the drug CID: 122677576 is a potent candidate for treating JIA. The pharmacophore study revealed that the drug CID: 122677576 is a non-inhibitor of CYP450 microsomal enzymes and was found to be non-toxic, similar to the established drug Methotrexate (CID: 126941). It has a lower LD50 value of 2.6698mol/kg as compared to the established compound having LD50 value as 23.4955mol/kg. Moreover, the compound was found to be non-carcinogenic.

Insights from the sequence similarity of Zika virus proteins with the Human nerve proteins

Massive peptide sharing between the Zika virus polyprotein and host tissue proteins could elicit significant host-pathogen interactions and cross-reactions leading to autoimmune diseases. This study found similarities in the Zika V proteins and human nerve tissue proteins. 63 human nerve proteins were screened for similarities with the Zika V of which Neuromodulin, Nestin, Galanin, Bombesin, Calcium-binding protein were found to have similarities to the Zika V poly protein C at different sequence regions. These sequence similarities could be significant in regulating pathogenic interactions/autoimmunity, as Polyprotein C is known to be a virulent factor.