Pharmacophoric Features Research Articles

Structure optimization and molecular dynamics studies of new tumor-selective s-triazines targeting DNA and MMP-10/13 for halting colorectal and secondary liver cancers

A series of triazole-tethered triazines bearing pharmacophoric features of DNA-targeting agents and non-hydroxamate MMPs inhibitors were synthesized and screened against HCT-116, Caco-2 cells, and normal colonocytes by MTT assay. 7a and 7g surpassed doxorubicin against HCT-116 cells regarding potency (IC50 = 0.87 and 1.41 nM) and safety (SI = 181.93 and 54.41). 7g was potent against liver cancer (HepG-2; IC50 = 65.08 nM), the main metastatic site of CRC with correlation to MMP-13 expression. Both derivatives induced DNA damage at 2.67 and 1.87 nM, disrupted HCT-116 cell cycle and triggered apoptosis by 33.17% compared to doxorubicin (DNA damage at 0.76 nM and 40.21% apoptosis induction). 7g surpassed NNGH against MMP-10 (IC50 = 0.205 μM) and MMP-13 (IC50 = 0.275 μM) and downregulated HCT-116 VEGF related to CRC progression by 38%. Docking and MDs simulated ligands-receptors binding modes and highlighted SAR. Their ADMET profiles, drug-likeness and possible off-targets were computationally predicted.

Targeting N-methyl-lysine histone demethylase KDM4 in cancer: natural products inhibitors as a driving force for epigenetic drug discovery.

KDM4A-F enzymes are a subfamily of histone demethylases containing the Jumonji C domain (JmjC) using Fe(II) and 2-oxoglutarate for their catalytic function. KDM4 enzymes are overexpressed or deregulated in cancer, thus leading to alteration in chromatin structure and transcriptional defects. As KDM4 enzymes have been associated with malignancy, they may represent novel targets for developing innovative therapeutic tools to treat different solid and blood tumors, of note, KDM4A is the isozyme most frequently associated with aggressive phenotypes of these tumors. To this aim, industrial and academic medicinal chemistry efforts have identified different KDM4 inhibitors. In most cases, these are pan-KDM4 inhibitors, with low selectivity against other Jumonji family members. The pharmacophoric features of the inhibitors frequently include a chelating group capable of coordinating the catalytic iron within the active site of the KDM4 enzyme. Nonetheless, non-chelating compounds have also demonstrated promising inhibitory activity, suggesting potential flexibility in the drug design. Several natural products, containing monovalent or bivalent chelators, have been identified as KDM4 inhibitors, albeit with a micromolar inhibition potency. This highlights the potential for leveraging them as templates for the design and synthesis of new derivatives, exploiting nature's chemical diversity to pursue more potent and selective KDM4 inhibitors.

ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring.

Efficient virtual screening techniques are critical in drug discovery for identifying potential drug candidates. We present an open-source package for molecular alignment and 3D similarity calculations optimized for large-scale virtual screening of small molecules. This work parallels widely used proprietary tools and offers an approach complementary to structure-based virtual screening. Our package employs the PAPER software for optimizing molecular alignments based on Gaussian volume overlaps. GPU acceleration is utilized to significantly reduce computational time and resource requirements. After obtaining the optimal alignments between the target and the query molecules, both shape and color (based on pharmacophore features) scores are computed to assess molecular similarity, with aligned molecules optionally being output in sdf format. The package was benchmarked using the DUDE-Z public data sets. Results demonstrated the package's near-state-of-the-art performance and robustness across multiple target classes, with speed that enables many routine ligand-based drug discovery workflows. As an open-source and freely available resource (github.com/molecularinformatics/roshambo) with both a convenient Python API and command line interface, our package also addresses the need for accessible and efficient virtual screening tools in drug discovery.

Integration of Consensus‐Based Pharmacophore Mapping and Molecular Docking in Sequential Virtual Screening: Toward the Discovery of Novel PI3Kγ Inhibitors

AbstractNumerous research studies have demonstrated the significant correlation of phosphatidylinositol‐3 kinase gamma (PI3Kγ) with the onset and progression of various human diseases, highlighting PI3Kγ as a promising therapeutic target. However, PI3Kγ demonstrates considerable similarity with other isoforms in the PI3K family, presenting significant challenges in the creation of PI3Kγ inhibitors. This study presents an ensemble‐based virtual screening approach to discover novel inhibitors targeting PI3Kγ. Eganelisib (IPI‐549) is the sole selective PI3Kγ inhibitor that has progressed to clinical trials, making it a significant model for the advancement of novel PI3Kγ inhibitors. Initially, common feature pharmacophore and receptor–ligand pharmacophore models were independently developed using IPI‐549 and its potent derivatives, in conjunction with the crystal complex of PI3Kγ/IPI‐549. Both qualitative pharmacophore models proved highly effective at distinguishing between active and inactive compounds. Then, four widely utilized docking programs were chosen for assessment, where the Glide_SP mode demonstrated superior predictive accuracy in sampling ligand conformations during binding, effectively distinguishing between PI3Kγ inhibitors and noninhibitors. Finally, a virtual screening protocol was conducted to screen the ChEMBL database, utilizing similarity search, consensus‐based pharmacophore mapping, and sequential molecular docking. This process resulted in the identification of multiple molecules exhibiting notable promise as potent PI3Kγ inhibitors.

Ligand-based pharmacophore modeling targeting the fluoroquinolone antibiotics to identify potential antimicrobial compounds

Antibiotic resistance presents a serious challenge to global healthcare, making the discovery of new therapeutic agents crucial. In this study, we used pharmacophore modeling and virtual screening to identify potential lead compounds against drug-resistant bacteria. We developed a shared feature pharmacophore (SFP) map using four antibiotics—Ciprofloxacin, Delafloxacin, Levofloxacin, and Ofloxacin—and generated a drug library of 160,000 compounds from ZINCPharmer based on these features, which included hydrophobic areas, hydrogen bond acceptors (HBA), hydrogen bond donors (HBD), and aromatic moieties (Ar). Through virtual screening, we identified 25 potential drug compounds as hits, with fit scores ranging from 97.85 to 116 and RMSD values from 0.28 to 0.63. These hits were then subjected to molecular docking against the DNA gyrase subunit A protein (PDB ID: 4DDQ), with ciprofloxacin as a control. The top five compounds—ZINC09133461, ZINC03791737, ZINC21983587, ZINC26469742, and ZINC26740199—achieved the highest docking scores, ranging from − 7.3 to − 7.4 kcal/mol and ciprofloxacin − 7.3 kcal/mol. After evaluating the drug-likeness of these compounds using Lipinski’s rule and analyzing their physicochemical properties, ZINC26740199 emerged as the most promising lead, offering hope in the fight against antibiotic resistance. Furthermore, molecular scaffold analysis revealed key similarities between ZINC26740199 and Ciprofloxacin, particularly in aromatic rings, hydrophobic regions, and hydrogen bond acceptors. These features suggest its potential as an effective antimicrobial agent, though further laboratory studies are needed to confirm its efficacy.

Cheminformatics-driven prediction of BACE-1 inhibitors: Affinity and molecular mechanism exploration

The β-secretase, sometimes referred to as BACE1 or Asp2, is the enzyme responsible for initiating the production of Aβ by breaking down the amyloid precursor protein. Hence, BACE is a pivotal target for pharmacological intervention aimed at diminishing the production of Aβ in Alzheimer's disease (AD). We did a quantitative structure-activity relationship (QSAR) study on 1235 compounds that had been experimentally reported as BACE-1 inhibitors (Ki) to find the target molecule and structural patterns linked to blocking the BACE-1 receptor. The OECD-recommended genetic algorithm-multiple linear regression (GA-MLR) QSAR model strikes a good balance between being able to make accurate predictions and understanding how things work. It achieves high values for many evaluation metrics, including R2tr = 0.8047, Q2LMO = 0.802, R2ex = 0.805, CCCex = 0.891, Q2-F1=0.801, Q2-F2=0.799, and Q2-F3=0.815. The mechanistic interpretation of QSAR has identified some nitrogen atoms that are required to block beta-secretase and make it less effective at doing its job. A positively charged aromatic carbon atom has a more significant impact on beta-secretase-1 inhibition. The docking study showed that the catalytic dye residues Asp32 and Asp228 become protonated when compound 27 is present, but they stay unprotonated when compound 27 is not present. These rings of pyrazine and pyridine interact hydrophobically with Tyr71 and Ile118 residues, confirming the pharmacophoric features seen in the QSAR data. We examined the stability of both the protein-ligand complex and the apo-protein. The apoprotein had an average gyration radius of 22.13, whereas the protein-ligand complex had an average gyration radius of 22.91. No changes were made to the results from the molecular docking, molecular dynamics (MD) simulation, MMGBSA (Molecular Mechanics Generalized Born Surface Area), or DFT analyses. Therefore, the current work could effectively contribute to the future development of BACE inhibitors in medication design.

Synthesis, molecular modelling, and biological evaluation of novel quinoxaline derivatives for treating type II diabetes

Quinoxalines are benzopyrazine derivatives with significant therapeutic impact in the pharmaceutical industry. They proved to be useful against inflammation, bacterial, fungal, viral infection, diabetes and other applications. Very recently, in January 2024, the FDA approved new quinoxaline containing drug, erdafitinib for treatment of certain carcinomas. Despite the diverse biological activities exhibited by quinoxaline derivatives and the role of secretory phospholipase A2 (sPLA2) in diabetes-related complications, the potential of sPLA2-targeting quinoxaline-based inhibitors to effectively address these complications remains unexplored. Therefore, we designed novel sPLA2- and α-glucosidase-targeting quinoxaline-based heterocyclic inhibitors to regulate elevated post-prandial blood glucose linked to patients with diabetes-related cardiovascular complications. Compounds 5a–d and 6a–d were synthesised by condensing quinoxaline hydrazides with various aryl sulphonyl chlorides. Biological screening revealed compound 6a as a potent sPLA2 inhibitor (IC50 = 0.0475 µM), whereas compound 6c most effectively inhibited α-glucosidase (IC50 = 0.0953 µM), outperforming the positive control acarbose. Moreover, compound 6a was the best inhibitor for both enzymes. Molecular docking revealed pharmacophoric features, highlighting the importance of a sulfonohydrazide moiety in the structural design of these compounds, leading to the development of potent sPLA2 and α-glucosidase inhibitors. Collectively, our findings helped identify promising candidates for developing novel therapeutic agents for treating diabetes mellitus.

In vitro and In silico Antibacterial Evaluation of N-Methyl-2-phenylmaleimides

Background: Novel antibiotics are needed to stem the rise of antimicrobial resistance. N-Methyl-2-phenylmaleimide (NMP) compounds previously synthesised by our research group are structural analogues of 2,3,5-substituted perhydropyrrolo[3,4-d]isoxazole-4,6-diones found by others to have antibacterial activity. Objectives: This study aims to explain the significance of NMPs and their antibacterial activity. The antibacterial activity of the NMPs was determined against Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. The partition coefficient of the NMPs and a pharmacophore model were used to explain their antibacterial activity. Methods: The Kirby Bauer Disc diffusion method was used to screen the NMPs for activity, while the broth microdilution method was used to determine the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the active NMPs. Using the in vitro antibacterial activity of 2,3,5-substituted perhydropyrrolo[3,4-d]isoxazole-4,6-diones, a common feature pharmacophore model was constructed and validated. The rank score, fit value, enrichment factor (EF20%), and receiver operating characteristic area under the curve (ROC-AUC) were used as validation metrics. Results: The NMPs were only active against S. aureus, with compound 3 (4 µg/ml) being the most active. The majority of NMPs were bacteriostatic. A common feature pharmacophore model was validated (rank score: 120.5; fit value: 4; EF20%: 4.3; ROC-AUC: 0.9 ± 0.03) and showed that three hydrogen bond acceptors and a ring aromatic region are important for activity. Comparing the partition coefficient of the NMPs to their MIC a statistically significant correlation was found. Conclusion: NMPs can be used as lead compounds in future studies. The validated pharmacophore model and partition coefficient can be used to develop more active compounds.

Biological and Computational Studies of Hydrazone based Transition Metal(II) Complexes.

In the chronicles of human history, infectious diseases played a pivotal role, influencing societies, steering advancements in medicine, and significantly impacting the well-being of people worldwide. Consequently, in the pursuit of identifying effective combating agents for infectious ailments, the Co(II), Ni(II), Cu(II), Zn(II) complexes of N'-(4-nitrobenzylidene)benzohydrazide were synthesized in the current investigation. Numerous spectral and physical analysis were conducted to characterize the compounds which revealed octahedral stereochemistry of complexes. The anti-tuberculosis, anti-inflammatory, antibacterial and antifungal investigations demonstrated that the compounds (1-5) have significant efficacy for these infectious ailments. The [Zn(L)2(H2O)2] complex (5) has comparable TB inhibition potency to streptomycin as shown by MIC value of 0.0196 ± 0.0003 µmol/mL. Additionally, the anti-inflammatory, antibacterial and antifungal studies also revealed the comparable inhibiting property of (5) to standard drugs with significant IC50 (07.49 ± 0.08 µM) and MIC (0.0098 µmol/mL) values. Furthermore, pharmacophore modeling with addition of molecular docking, DFT, MESP, ADMET were employed against (1-5) to give a new insight in biological evaluations. The pharmacophore modeling suggested that (5) has a distinctive pharmacophoric features including cationic sites, hydrogen-bond donors and acceptors which provide valuable insights into drug design for pharmacological applications. Moreover, another in silico investigations authenticate the bioactivity of (5).

Potent Small Molecules Inhibitors Discovery through Ligand-based Modelling for Effective Treatment of Parkinson’s Disease

Background: Parkinson’s disease (PD) is a chronic neurodegenerative disease affecting mostly aged people. The disease's symptoms develop gradually over time and include tremors, bradykinesia, rigidity, and postural instability. Current treatment options for PD are only symptom-targeted. Prolyl oligopeptidase (POP) is a serine protease enzymes implicated in PD pathogenesis via an increase in the aggregation of α-synuclein protein in the brain. Aim: This study aims to identify potent anti-PD ligands with inhibitory potential against POP Methods: Ligand-based pharmacophore modeling, Glide extra precision (XP) docking, and post-simulation analysis methods were used. Results: The adopted ligand-based (LB) modeling generated pharmacophoric features, including 1 hydrophobic group, 1 positive ionizable group, 2 aromatic rings, and 2 hydrogen bond acceptors. A total of 23 hits with a Gunner-Henry score of 0.7 and an enrichment factor of 30.24 were obtained as validation protocols, making it an ideal model. The LB model retrieved 177 hit compounds from the 69,543 natural screening ligands available in the Interbioscreen database. Interestingly, ligands 1, 2, 3, 4, and 5 orderly demonstrated higher binding affinities with Glide XP docking of -9.0, -8.8, -8.7, -8.7, -8.7 kcal/mol compared to reference drugs, GSK552 and ZPP with -8.2, and -6.8 kcal/mol respectively. Similarly, their MM/GBSA values were recorded as -54.4, -51.3, -58.4, -49.3, - 33.5, & -32.5 kJ/mol respectively. Further, MD analysis indicated that ligands had higher favorable binding and stability to the receptor. Conclusion: Overall, the study paves the way for developing potential anti-PD therapeutics. The ligands are recommended as adjuvant/single candidate as anti-PD candidates upon further experiment.

N-acyl-4-arylaminopiperidines: Design and synthesis of a potential antimicrobial scaffold

We report a concise synthesis of N-acylated piperidines through a Knoevenagel-Doebner condensation/amide construction/ amination sequence. The design of the piperidines considered the pharmacophoric features found in previously reported inhibitors of FabI, an enzyme implicated in bacterial fatty acid biosynthesis. After the microbiological evaluation at 50 μM, the analogs displayed moderate activity against some pathogens from the ESKAPE group, reaching up to 42 % of growth inhibition for MRSA, 54 % for K. pneumoniae, and 37 % for P. aeruginosa (multiresistant strains). Docking studies demonstrate that almost all of them docked satisfactorily into the catalytic domain of S. aureus FabI, maintaining a similar pose as other reported inhibitors. The results shown herein propose the N-acyl-4-arylaminopiperidines as the basis for the development of more active candidates.

Flavopiridol inhibits adipogenesis and improves metabolic homeostasis by ameliorating adipose tissue inflammation in a diet-induced obesity model

Repositioning of FDA approved/clinical phase drugs has recently opened a new opportunity for rapid approval of drugs, as it shortens the overall process of drug discovery and development. In previous studies, we predicted the possibility of better activity profiles of flavopiridol, the FDA approved orphan drug with better fit value 2.79 using a common feature pharmacophore model for anti-adipogenic compounds (CFMPA). The present study aimed to investigate the effect of flavopiridol on adipocyte differentiation and to determine the underlying mechanism. Flavopiridol inhibited adipocyte differentiation in different cell models like 3T3-L1, C3H10T1/2, and hMSCs at 150 nM. Flavopiridol was around 135 times more potent than its parent molecule rohitukine. The effect was mediated through down-regulation of key transcription factors of adipogenesis i.e. Peroxisome proliferator-activated receptor gamma (PPARγ), CCAAT/enhancer-binding protein alpha (C/EBPα), and their downstream targets, including adipocyte protein −2 (aP2) and fatty acid synthase (FAS). Further, results revealed that flavopiridol arrested the cell cycle in G1/S phase during mitotic clonal expansion by suppressing cell cycle regulatory proteins i.e. Cyclins and CDKs. Flavopiridol inhibited insulin-stimulated signalling in the early phase of adipocyte differentiation by downregulation of AKT/mTOR pathway. In addition, flavopiridol improved mitochondrial function in terms of increased oxygen consumption rate (OCR) in mature adipocytes. In the mouse model of diet-induced obesity, flavopiridol attenuated obesity-associated adipose tissue inflammation and improved serum lipid profile, glucose tolerance as well as insulin sensitivity. In conclusion, the FDA approved drug flavopiridol could be placed as a potential drug candidate for the treatment of cancer and obesity comorbid patients.

Chemical Methods for the Construction of Spirocyclic β-Lactams and Their Biological Importance

AbstractSpirocyclic β-lactams are a family of natural and synthetic chemicals with different biological activities, including antibacterial properties, and interact with critical physiological targets such as T-type calcium channels and acetyl-CoA cholesterol acyltransferase. Their unique chemical structure, combining a spiro ring system with a β-lactam group, offers promising opportunities for the targeted discovery of medications in medicinal chemistry. Spirocyclic β-lactams have the potential to be adaptable frameworks for developing novel therapeutic medicines with particular three-dimensional pharmacophoric characteristics and increased biological efficacy. Numerous methods are employed for the synthesis of spirocyclic β-lactams, such as cyclization, functional group modifications, asymmetric synthesis utilizing chiral catalysts and biomimetic approaches. In this short review, two distinct approaches describing recent syntheses of spirocyclic β-lactams (from 2021 to 2024) are discussed. The first is based on constructing the β-lactam ring, while the other entails transforming monocyclic β-lactams into spirocyclic structures. These methods include detailed reaction processes and descriptions of the biological functions of the target spirocycles. The applications of spirocyclic β-lactams in medicinal chemistry highlight their role in the synthesis of structurally diverse compounds with significant therapeutic potential, demonstrating creative chemical methods for building complex molecular structures.1 Introduction2 β-Lactam Ring Synthesis3 Non-β-Lactam Ring Synthesis4 Miscellaneous Examples5 Conclusion and Outlook

Antibacterial activity of natural flavones against bovine mastitis pathogens: in vitro, SAR analysis, and computational study

Bovine mastitis is a worldwide disease affecting dairy cattle and causes major economic losses in the dairy industry. Recently, the emergence of microbial resistance to the current antibiotics complicates the treatment protocol which necessitates antibiotic stewardship and further research to find new active compounds. Recently, phytobiotics have gained interest in being used as an alternative to antibiotics in the poultry industry as an antibiotic stewardship intervention. This study evaluated the in vitro antibacterial activity of 16 flavonoids against bovine mastitis pathogens. Two flavones: 2-(4-methoxyphenyl)chromen-4-one (1) and 2-(3-hydroxyphenyl)chromen-4-one (4) showed inhibition of the growth of Klebsiella oxytoca with MIC values range (25–50 µg mL− 1) followed by a structure-activity relationship (SAR) study indicating that the presence of a hydroxyl group at C-3` or methoxy at C-4` increases the activity against Klebsiella oxytoca while the presence of hydroxyl group at C-7 decreases the activity. Furthermore, a structure-based drug development approach was applied using several in silico tools to understand the interactions of active flavones at the active site of the DNA gyrase protein. Compound (4) showed a higher docking score than quercetin (standard) which is known to have antibacterial activity by inhibiting the DNA gyrase. In addition, the structure-based pharmacophores of compound (4) and quercetin showed similar pharmacophoric features and interactions with DNA gyrase. Based on our findings, compounds (1) and (4) are promising for further study as potential anti-microbial phytochemicals that can have a role in controlling bovine mastitis as well as to investigate their mechanism of action further.

Design and Efficient Synthesis of New 4-Amino-Substituted 2-(4-Bromobenzyl)-5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidines of Anticancer Interest and Their In Silico Study

AbstractThienopyrimidines are an emerging class of fused pyrimidines due to their broad spectrum of pharmacological properties, including antimicrobial, anti-inflammatory, antimalarial, anticancer, etc. The anticancer activity of these compounds has been mechanistically proven via the inhibition of validated drug targets, such as EGFR, VEGFR-2, PI3K, and c-kit. In this research article, we designed and synthesized new 4-amino-substituted 2-(4-bromobenzyl)-5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidines to explore their anticancer potential. These heterocycles were designed based on pharmacophoric features of the core heterocycle, varying its C4 substitution with a variety of amines and considering cancer protein-ligand interactions with the aim to obtain potent lead molecules. The target compound-protein interaction complexes were analyzed, and lead compounds were identified based on their better binding affinity in molecular docking studies.

Development of New N-{4-[(7-Chloro-5-methylpyrrolo[2,1-f] [1,2,4]triazin-4-yl)oxy]-3-fluorophenyl}benzenesulfonamide Analogues: Exploring Anticancer Potential through MerTK Inhibition

AbstractMer proto-oncogene tyrosine-protein kinase (MerTK), a part of the TAM (TYRO3, AXL, and MerTK) family, is directly correlated with metastasis and various types of cancers. The inhibition of this receptor is a promising strategy for more-effective chemotherapy. Considering the pharmacophoric features of the active domain of MerTK and the structural characteristics of the investigational drug BMS794833, we designed five new N-{4-[(7-chloro-5-methylpyrrolo[2,1-f][1,2,4]triazin-4-yl)oxy]-3-fluorophenyl}benzenesulfonamide analogues. In cytotoxicity studies, one of the analogues displayed a significantly higher cytotoxicity than cisplatin. It showed IC50 values of 2.09, 1.96, and 3.08 μM against A549, MCF-7, and MDA-MB-231 cancer cell lines, respectively. In drug metabolism and pharmacokinetic studies, it was the most stable analogue and displayed a moderate MerTK inhibitory potential. Molecular-docking studies were performed to corroborate the MerTK inhibition, and the same analogue achieved the most significant docking score (–12.33 kcal/mol). Docking interactions demonstrated that the imine and amine group of the 3-chloropyridine moiety of BMS794833 formed hydrogen bonds with the main chain of the ATP pocket residue Met674, while the oxygen atoms of the 4-oxo-1,4-dihydropyridine-3-carboxamide moiety established hydrogen bonds with the Lys619 and Asp741 amino acid residues of the allosteric pocket of MerTK protein. These promising results provide evidence that the N-{4-[(7-chloro-5-methylpyrrolo[2,1-f][1,2,4]triazin-4-yl)oxy]-3-fluorophenyl}benzenesulfonamide pharmacophore can give potential insights into the development of new MerTK inhibitors.

IDENTIFICATION OF NEW CHEMICAL ENTITIES AS VHL INHIBITORS FOR DIABETIC WOUND HEALING

Diabetes is a kind of endocrine disease that impacts around 6% of the world's population. Globally, 68% of amputations were performed in persons with diabetes. Hypoxia-inducible factor 1-alpha (HIF-1) is a crucial regulator of wound healing in diabetic patients, which includes epithelialization, angiogenesis, granulation, tissue development, and wound contraction. Even though diabetic wounds are hypoxic, HIF-1 levels are decreased during diabetic conditions. Diabetic wound healing necessitates the modulation of hypoxia-induced responses by VHL–HIF-1 protein-protein inhibition (PPI). Our proposed hypothesis is to increase HIF-1 levels by inhibiting VHL and HIF-1 interactions by small bioactive molecules, accelerating diabetic wound healing. Three features (Two hydrogen bond acceptors and One hydrogen bond donor) pharmacophore model was generated from the existing VHL inhibitors. Virtual screening was done based on the generated pharmacophore, and a library of 700 compounds was selected using ZINCPharmer. Based on the docking analysis the Top 15 HITs were selected & after performing ADMET studies, the Top 2 HITs (ZINC04214700 and ZINC12529886) were identified as potential VHL inhibitors. From this finding, we demonstrated that inhibiting the VHL and HIF-1 connection is a promising strategy for treating diabetic wounds.

Lead Identification Through In Silico Studies: Targeting Acetylcholinesterase Enzyme Against Alzheimer's Disease.

In this work, we aimed to acquire the best potential small molecule for Alzheimer's disease (AD) treatment using different models in Biovia Discovery Studio to identify new potential inhibitors of acetylcholinesterase (AChE) via in silico studies. The prevalence of cognitive impairment-related neurodegenerative disorders, such as AD, has been observed to escalate rapidly. However, we still know little about the underlying functions, outcome predictors, or intervention targets causing AD. The objective of the study was to optimize and identify the lead compound to target AChE against Alzheimer's disease. Different in silico studies were employed, including the pharmacophore model, virtual screening, molecular docking, de novo evolution model, and molecular dynamics. The pharmacophoric features of AChE inhibitors were determined by ligand-based pharmacophore models and 3D QSAR pharmacophore generation. Further validation of the best pharmacophore model was done using the cost analysis method, Fischer's randomization method, and test set. The molecules that harmonized the best pharmacophore model with the estimated activity < 1 nM and ADMET parameters were filtered, and 12 molecules were subjected to molecular docking studies to obtain binding energy. 3vsp_EK8_1 secured the highest binding energy of 65.60 kcal/mol. Further optimization led to a 3v_Evo_4 molecule with a better binding energy of 70.17 kcal/mol. The molecule 3v_evo_4 was subjected to 100 ns molecular simulation compared to donepezil, which showed better stability at the binding site. A lead compound, 3v_Evo_4 molecule, was identified to inhibit AChE, and it could be further studied to develop as a drug with better efficacy than the existing available drugs for treating AD.

Structure-based pharmacophore modeling for precision inhibition of mutant ESR2 in breast cancer: A systematic computational approach.

Breast cancer, a leading cause of female mortality, is closely linked to mutations in estrogen receptor beta (ESR2), particularly in the ligand-binding domain, which contributed to altered signaling pathways and uncontrolled cell growth. This study investigates the molecular and structural aspects of ESR2 mutant proteins to identify shared pharmacophoric regions of ESR2 mutant proteins and potential therapeutic targets aligned within the pharmacophore model. This study was initiated by establishing a common pharmacophore model among three mutant ESR2 proteins (PDB ID: 2FSZ, 7XVZ, and 7XWR). The generated shared feature pharmacophore (SFP) includes four primary binding interactions: Hydrogen bond donors (HBD), hydrogen bond acceptors (HBA), hydrophobic interactions (HPho), and Aromatic interactions (Ar), along with halogen bond donors (XBD) and totalling 11 features (HBD: 2, HBA: 3, HPho: 3, Ar: 2, XBD: 1). By employing an in-house Python script, these 11 features distributed into 336 combinations, which were used as query to isolate a drug library of 41,248 compounds and subjected to virtual screening through the generated SFP. The virtual screening demonstrated 33 hits showing potential pharmacophoric fit scores and low RMSD value. The top four compounds: ZINC94272748, ZINC79046938, ZINC05925939, and ZINC59928516 showed a fit score of more than 86% and satisfied the Lipinski rule of five. These four compounds and a control underwent molecular (XP Glide mode) docking analysis against wild-type ESR2 protein (PDB ID: 1QKM), resulting in binding affinity of -8.26, -5.73, -10.80, and -8.42 kcal/mol, respectively, along with the control -7.2 kcal/mol. Furthermore, the stability of the selected candidates was determined through molecular dynamics (MD) simulations of 200 ns and MM-GBSA analysis. Based on MD simulations and MM-GBSA analysis, our study identified ZINC05925939 as a promising ESR2 inhibitor among the top four hits. However, it is essential to conduct further wet lab evaluation to assess its efficacy.

Pharmacophore guided deep learning approach to identify novel inhibitors targeting mycobacterial polyketide synthase Pks13-TE domain

Tuberculosis (TB), an enduring global health challenge, persists due to the rise of drug-resistant Mycobacterium tuberculosis (MTB) strains. Among potential therapeutic targets, Pks13, a protein crucial for mycolic acid biosynthesis, is key for Mtb's virulence and survival. This study employed a pharmacophore-based drug design approach, employing the Pharmacophore-Guided Molecular Generation (PGMG) tool to target Pks13 inhibitors. Aromatic, hydrophobic, positive ion and hydrogen bond acceptors pharmacophoric features were identified from co-crystal ligands. Candidate compounds underwent evaluation of pharmacokinetic properties with the ADMET_AI tool. Further refinement involved molecular docking with PLANTS software, absolute binding free energy calculations via KDeep, and toxicity assessments using eToxPred. MM-GBSA, PCA, DCCM, and FEL were incorporated to validate and refine inhibitors accurately. From this analysis, we discovered five novel hit molecules. These includes, ethyl (S)-4-(4-(2-(2-(cyclohexylamino)-2-oxoethoxy)-2-oxoethoxy)phenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (Pk1), 2-(4-((2‑butyl‑6-pivalamido-1H-benzo [d]imidazol-1-yl)methyl)phenoxy)acetic acid (Pk2), (S)-2-(4-(4-cyclopentyl-5-(1-((6-methyl-2-morpholinopyrimidin-4-yl)amino)ethyl)-4H-1,2,4-triazol-3-yl)phenoxy)acetic acid (Pk3), (E)-2-(4-oxo-5-(4-((6-phenylpyridin-2-yl)methoxy)benzylidene)-2-thioxothiazolidin-3-yl)acetic acid (Pk4), and N-((1R,4r)-4-(((1R,2r,3S,5S,7S)-5‑hydroxy adamantan-2-yl)oxy)cyclohexyl)-4-morpholinobenzamide (Pk5). We conclude that the screened hit compounds may act as potential inhibitors targeting Pks13 and further preclinical and clinical studies may pave the way for developing them as effective therapeutic agents for the treatment of MTB.