Lead Molecules Research Articles

Phyto-pharmacological Evaluation of Pimenta dioica (Linn.) Merill, Essential oil for Anthelmintic and Antimicrobial potential

Pimenta dioica (Linn.) Merill., belongs to the family Myrtaceous, has been used as a spice and is well known for its culinary as well as medicinal values. The aim of the current study was to assess the in vitro antimicrobial, anthelmintic activity and phytochemical composition of the essential oil extracted from Pimenta dioica leaves. The extraction of essential oil was performed with the Clevenger apparatus, by hydro-distillation. Pimenta dioica essential oil yield was 1.03%. The GC-MS analysis of this Pimenta dioica essential oil showed that eugenol (74.72%) was the predominant component. The essential oil showed potent anthelmintic activity assay when analysed by the adult worm’s motility assay. It has shown a comparable paralysis and disintegration profile of the model organism to that of the standard drug albendazole. The essential oil was also found to be effective against common human pathogenic bacteria, including Staphylococcus aureus, Klebsiella, Escherichia coli, Chromobacterium violaceum and Proteus vulgaris. It also showed moderate antifungal activity against Candida albicans and Aspergillus niger. These results proved that Pimenta dioica essential oil could be used as a source of the lead molecule for developing novel anthelmintic or antimicrobial agents.

Screening of Potential Phytochemicals for the Identified Candidate Virulence Proteins in Enterobacter huaxiensis

ABSTRACT: Enterobacter huaxiensis, a novel gram-negative bacterium of the family Enterobacteriaceae, was recovered from the blood of the patients at West China Hospital. The present study aims to predict potential lead molecules against the identified virulence-associated antibiotic-resistant protein for drug designing. Two virulence-associated antibiotic-resistance proteins belonging to the OqxAB efflux protein family of the RND superfamily were identified in the pathogen using bioinformatics tools/databases. Based on the structure prediction by homology modeling and validations, the RND transporter permease subunit, OqxB was selected as the potential target for lead identification. The binding pocket of the target protein was calculated using CASTp. A total of 204 phytochemicals were screened virtually to obtain compounds that had better binding affinity, drug-likeness and pharmacokinetic potential to be used as safe ligands against the target protein. Among these, Chrysoeriol, Isopimaric acid, Baicalein and Biochanin A were found to be within the permissible range of Lipinski rule of five for drug-likeness, possessing better ADMET properties, and lower target-protein binding energy (less than -8.0 kcal/mol). Ligand-protein docking showed stable non-covalent interactions between active site residues and ligands. Thus, these compounds may be considered potential inhibitors of the target protein that may inactivate the efflux pump and restore antibiotic sensitivity.

Unlocking potential diabetes therapeutics: Insights into alpha-glucosidase inhibition

Diabetes mellitus (DM) stands as a significant global health challenge, ranking third among causes of mortality worldwide. Despite extensive endeavors, effective treatments for diabetes remain elusive. Alpha-glucosidase, a pivotal enzyme in glycoprotein metabolism regulation, emerges as a promising therapeutic target for mitigating postprandial hyperglycemia, a hallmark of diabetes. In this study, we employed advanced computational methodologies to identify inhibitors of lysosomal α-glucosidase. Leveraging pharmacophore-based virtual screening of a vast library of drug-like molecules, we unearthed 161 potential inhibitors capable of binding within the enzyme's active pocket. Subsequent molecular docking simulations yielded five lead molecules exhibiting robust binding affinities and favorable interaction profiles with critical catalytic residues. Further analysis through molecular dynamics simulations provided crucial insights into the stability and conformational dynamics of the inhibitor-enzyme complexes. Notably, certain residues emerged as pivotal for the retention of inhibitors within the active site. Our findings underscore the potential of LIG1-LIG5 as promising inhibitors against lysosomal α-glucosidase, presenting novel avenues for the development of effective diabetes therapeutics. This research enriches our understanding of the molecular underpinnings of diabetes treatment, facilitating targeted drug development strategies in the quest for improved patient outcomes.

Molecular Optimization Model with Patentability Constraint

In drug development, molecular optimization is a crucial challenge that involves generating novel molecules given a lead molecule as input. The task requires maintaining molecular similarity to the original molecule while simultaneously optimizing multiple chemical attributes. To aid in this process, numerous generative models have been proposed. However, in practical applications, it is crucial for these models not only to generate novel molecules with the above constraints but also to generate molecules that significantly differ from any existing patented compounds. In this work, we present a multi-optimization molecular framework to address this challenge. Our framework trains a model to prioritize both enhanced properties and substantial dissimilarity from patented compounds. By jointly learning continuous representations of optimized and patentable molecules, we ensure that the generated molecules are significantly distant from any patented compounds while improving chemical properties. Through empirical evaluation, we demonstrate the superior performance of our approach compared to state-of-the-art molecular optimization methods both in chemical property optimization and patentability.

Computational design and in vitro assay of lantadene-based novel inhibitors of NS3 protease of dengue virus

Abstract Dengue virus (DENV) infection is one of the diseases for which no drug is available for the treatment. The DENV NS2B-NS3 protease is considered to be the prime target for anti-dengue drug development because of its importance in the development of new virus subunits via DENV poly-protein breakdown. Pentacyclic triterpenoids (Lantadenes) from the weed Lantana camara L. and its semi-synthetic congeners have shown a wide array of biological activities in the last two decades. The virtual screening strategy was used on the library of 78 natural and semi-synthetic lantadenes to predict the potent antagonists for the NS2B-NS3 protease enzyme of DENV and their experimental validation by in vitro assay of lead molecules. In the in silico analysis of 78 triterpenoids, two lead molecules (−10.60 and −9.93 kcal/mol) were predicted to be inhibitors of protease (viral) when compared to its reference ligand 1,8-dihydroxy-4,5-dinitroanthraquinone (−5.377 kcal/mol). At the same time, binding affinity, pharmacokinetic, and toxicity profiling, along with molecular dynamics simulations, were studied. The in vitro viral infection inhibition assay inferred that lead molecule 62 exhibited a 60% and 45% reduction in DENV titers at 10 and 5 µM concentrations, respectively. The lead molecule 62 can further be optimized for its pharmacophore and has the potential to be developed as a drug-like molecule.

Guanidine-to-piperidine switch affords high affinity small molecule NPFF ligands with preference for NPFF1-R and NPFF2-R subtypes

The Neuropeptide FF (NPFF) receptor system is known to modulate opioid actions and has been shown to mediate opioid-induced hyperalgesia and tolerance. The lack of subtype selective small molecule compounds has hampered further exploration of the pharmacology of this receptor system. The vast majority of available NPFF ligands possess a highly basic guanidine group, including our lead small molecule, MES304. Despite providing strong receptor binding, the guanidine group presents a potential pharmacokinetic liability for in vivo pharmacological tool development. Through structure-activity relationship exploration, we were able to modify our lead molecule MES304 to arrive at guanidine-free NPFF ligands. The novel piperidine analogues 8b and 16a are among the few non-guanidine based NPFF ligands known in literature. Both compounds displayed nanomolar NPFF-R binding affinity approaching that of the parent molecule. Moreover, while MES304 was non-subtype selective, these two analogues presented new starting points for subtype selective scaffolds, whereby 8b displayed a 15-fold preference for NPFF1-R, and 16a demonstrated an 8-fold preference for NPFF2-R. Both analogues showed no agonist activity on either receptor subtype in the in vitro functional activity assay, while 8b displayed antagonistic properties at NPFF1-R. The calculated physicochemical properties of 8b and 16a were also shown to be more favorable for in vivo tool design. These results indicate the possibility of developing potent, subtype selective NPFF ligands devoid of a guanidine functionality.

Plumbagin as a preferential lead molecule to combat EGFR-driven matrix abundance and migration of cervical carcinoma cells.

The handshake between the complex networks of matrix components in the tumor micro-environment (TME) is considered as a crucial event in the progression of several cancers including cervical carcinoma (CC). A number of studies report a connection between epidermal growth factor (EGF) and matrix component production. Studies demonstrate that the mechano-transduction trigger by collagen, influences the tumor cells to undergo epithelial-mesenchymal transition (EMT) and block the entryof drugs. We hypothesize that the intervention to prevent EGF triggered deposition of matrix components could sensitize several therapies for CC cells. We utilized morphological assessment, MTT assay, mitored tracking, acridine orange (AO)/ ethidium bromide (EtBr) staining and bromodeoxyuridine (BrdU) assay to measure the cell viability, mitochondrial activity, cellular apoptosis, and DNA synthesis. Clonogenic assay and scratch healing assay were executed to address the stemness and migratory potential. Detection of glycosaminoglycan's (GAGs), collagen, matrix metalloproteinase (MMP)-2/9 secretion and calcium (Ca2+) ions were performed to assess the production of matrix components. Finally, the interaction between EGFR and plumbagin was evaluated by employing molecular dynamics (MD) simulation. Pre-treating the cells with plumbagin inhibited the EGF-induced EMT along with reduction in cell proliferation, migration, clonogenesis and depletion of matrix components. The actions of EGF and plumbagin were more pronounced in HPV-positive CC cells than HPV-negative CC cells. This study identified that increased matrix production triggered by EGF-rich milieu is inhibited by plumbagin in human papilloma viral (HPV) 68 positive ME180, HPV 16 positive SiHa and HPV-negative C33A cell lines. Delivery of plumbagin directly to TME would effectively accelerate the clearance of CC cells, reduce metastasis and matrix abundance by employing targeted delivery to minimize the undesired effects of plumbagin.

Abstract 6056: Identification of first-in-class, orally bioavailable SOS1 bifunctional degraders for the treatment of KRAS- and RTK-driven cancers

Abstract Monotherapies which target nodes within the RTK-RAS-MAPK pathway often display early potency in the clinic, but their preliminary response is limited as tumors begin to regrow due to adaptive and acquired resistance mechanisms. Disrupting proteins that mitigate either type of resistance mechanism in combination with oncogene-targeted agents could help extend and enhance the clinical potential of these drugs. Son of Sevenless 1 (SOS1), a RAS guanine nucleotide exchange factor, is a highly attractable protein to target given its role in transducing inputs from upstream receptor tyrosine kinases (RTKs) to downstream RAS proteins to regulate signaling pathways involved in cell proliferation and survival. Additionally, SOS1 is subject to MAPK-mediated negative feedback inhibition and drugs targeting upstream and downstream nodes relieves SOS1 from this inhibition resulting in pathway reactivation. To address this need, we have developed orally bioavailable SOS1 bifunctional degraders for cancers driven by KRAS and RTKs. Our top two lead molecules demonstrate CRBN- and proteasomal-mediated SOS1 degradation with DC50s < 10nM and maximum degradation > 90%. Consistent with this notion, SOS1 degradation inhibited downstream signaling marker phopshoERK with IC50s < 5nM and were 26- or 53-fold more potent when compared to the clinical SOS1 inhibitor. Notably, the SOS1 degraders exhibited weaker SOS1 binding compared to other SOS1 inhibitors highlighting that the potency is heavily driven by the catalytic nature of degradation rather than occupancy-driven events. Both SOS1 degraders displayed CRBN- and SOS1-dependent antiproliferative activity in KRAS- and EGFR- mutant, solid tumor cell lines as well as in BCR-ABL driven, CML cells with IC50 values ranging from 0.5-10nM. Consistent with our in vitro data, oral administration of our SOS1 degraders in mice harboring H358 (KRAS G12C) and H441 (KRAS G12V) xenografts resulted in SOS1 degradation, phosphoERK reduction and significant tumor growth inhibition. While SOS1 degrader monotherapy demonstrated in vitro and in vivo potency, combination of mutant or allele specific EGFR and KRAS inhibitors and ABL inhibitors with our proof-of-concept degraders prevented pathway reactivation associated with these inhibitors and lead to a more durable response. These combinations also yielded synergistic effects in in vitro proliferation assays as well as enhanced tumor growth inhibition in KRAS-mutant xenograft models. Together, our SOS1 degraders alone and in combination with other targeted agents demonstrated anti-tumor activity in a variety of KRAS- and RTK-driven cancer cell lines and xenograft models. These results support the potential of orally bioavailable SOS1 degraders to help mitigate pathway reactivation for enhanced efficacy and prolonged response duration. Citation Format: Kyle Begovich, Angela Schoolmeesters, Navin Rajapakse, Elena Martinez, Qiao Liu, Arvind Shakya, Akinori Okano, Venkat Mali, Shenlin Huang, Aparajita Chourasia, Leah Fung. Identification of first-in-class, orally bioavailable SOS1 bifunctional degraders for the treatment of KRAS- and RTK-driven cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6056.

Abstract 6051: Discovery of oral SMARCA2 degraders for the treatment of SMARCA4 mutant tumors

Abstract The paralog enzymes SMARCA2 and SMARCA4 are mutually exclusive members within the SWI/SNF chromatin remodeling complex. This complex plays a crucial role in governing gene expression by altering the chromatin and rendering it accessible to transcription machinery. The process of chromatin remodeling by the SWI/SNF complex is dependent on ATP hydrolysis. Within the complex, either SMARCA2 or SMARCA4 serves as the sole component capable of catalyzing ATP hydrolysis and are thereby essential to the activity of the complex. SMARCA4 has been found to be mutated in various cancer types, including non-small cell lung carcinoma, colon adenocarcinoma, bladder, and endometrial cancer. In cancer cells where SMARCA4 is deleted, the functionality of the SWI/SNF complex and cell survival is dependent on the presence of SMARCA2, thereby resulting in synthetic lethality if SMARCA2 is depleted. Utilizing in vitro and in vivo model systems we have discovered potent, selective, and orally bioavailable heterobifunctional degraders targeting SMARCA2. Our lead molecules exhibit potent and selective degradation of SMARCA2 (DC50 < 10 nM) with no impact on SMARCA4 (DC50 > 1000 nM). Furthermore, a striking selective activity in proliferation assays was observed with SMARCA4 deleted cells exhibiting gIC50 ranging from 1 -10 nM and SMARCA4 WT cells > 1000 nM. Oral administration in mice harboring human cancer cell line xenografts revealed dose-dependent and selective in vivo degradation of SMARCA2. Degradation of SMARCA2 led to significant anti-tumor activity in SMARCA4 mutant NSCLC xenograft models. Together, these data demonstrate a foundation for the development of a best-in-class degrader for the treatment of SMARCA4 deleted cancers. Citation Format: Jose C. Clemente, Lal Harikrishnan, Steve Knight, Debangshu Samanta, Zhenwu Li, Rakesh Nagilla, Nathan Kendsersky, Shreyas Joshi, Peter Orth, Matt Tudor, Qiaolin Deng, Clemente Aguilar-Bonavides, Elham Behshad, Zhihua Sui, Corey Strickland, Larry J. Jolivette, Helai P. Mohammad. Discovery of oral SMARCA2 degraders for the treatment of SMARCA4 mutant tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6051.

Abstract 7073: Integrating fragment-based crystallographic screening with dTAG-PROTAC degradation and genetic rescue to explore the function of eIF4E

Abstract The translation initiation factor eIF4E is a rate-limiting factor for protein synthesis that binds the mRNA m7G-cap to initiate the recruitment and binding of eIF4F components such as eIF4G. Targeting eIF4E has long been considered a promising anticancer strategy but it has remained undruggable using conventional screening approaches. Fragment-based crystallographic screening is a powerful technique for probing the surface of proteins to identify potentially druggable binding sites. Here, we describe fragment-based screening using a combination of Xray crystallography and NMR to identify low affinity fragment hits binding to the mRNA cap-binding site or at an additional site of unknown functional relevance (site 2). Subsequent rounds of iterative structure-based design yielded a lead molecule, with 100nM binding potency for site 2, that could disrupt the eIF4E:eIF4G interaction and inhibit cap-dependent translation in cell lysates. To explore the functional relevance of site 2 we established a cell model expressing an eIF4E-FKBP12F36V fusion protein that was sensitive to degradation following treatment with the heterobifunctional dTAGV-1 molecule. Degradation of eIF4E resulted in inhibition of cell growth and reduced expression of MCL1 protein, that were rescued by re-expression of a non-degradable wild-type eIF4E. A mutation reported to block canonical eIF4G binding (W73F) disrupted binding to eIF4G but to our surprise retained the ability to rescue the eIF4E degradation phenotype. Mutation of site 2 (L85R and L134R) also disrupted the eIF4E:eIF4G interaction. The L85R mutant remained able to partially rescue the cellular responses, in contrast to the L134R mutant that could not rescue eIF4E loss. The W73F/L85R double mutant resulted in a combinatorial loss of eIF4E function. Despite disrupting eIF4E function in lysates, there was a significant drop-off of compound activity in cells. However, treatment of the W73F mutant with compound recapitulated the combination of the W73F canonical eIF4G binding mutation with the L85R site 2 mutation. This approach demonstrates the power of coupling fragment screening with target-degradation and genetic rescue approaches to find and explore novel functional pockets. Our data suggest it may be necessary to disrupt the extended protein-protein interaction made by both the canonical and non-canonical regions of eIF4E to drive a strong functional effect in cells. However, the discovery of a lead compound, the associated structural understanding, and the knowledge that one site 2 mutation inactivates eIF4E provides hope that a significantly more potent small molecule inhibitor or degrader could drive a more profound cellular effect which may lead to improved cellular activity and a deeper understanding of eIF4E biology. Citation Format: Paul A. Clarke, Swee Y. Sharp, Marianna Martella, Christopher I. Milton, Charlotte East, Mladen Vinkovic, Nicola Wallis, George Ward, Caroline Richardson, Andrew Woodhead. Integrating fragment-based crystallographic screening with dTAG-PROTAC degradation and genetic rescue to explore the function of eIF4E [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7073.

Abstract 1230: MTX-531, a first-in-class pan-PI3K inhibitor spares hyperinsulinemia yielding durable tumor regressions and resilience to adaptive resistance

Abstract Adaptive resistance mechanisms compromise the long-term effectiveness of kinase-targeted agents dictating the need for strategic combination approaches. MTX-531 was computationally designed to selectively target both PI3K and wild type EGFR. MTX-531 exhibits low nanomolar potency against the PI3K isoform family and EGFR with a high degree of specificity predicted by co-crystal structural analyses. Full kinome screening confirmed that MTX-531 is exquisitely selective for its intended targets. We evaluated the pharmacological profile of MTX-531, whereupon single agent treatment with this lead molecule elicited a high incidence of durable tumor regressions in a broad panel of PIK3CA mutant CDX and PDX squamous head and neck (HNSCC) models. The combination of MTX-531 with RAS pathway inhibitors, including agents directed against KRAS G12C, led to durable regressions of KRAS mutant colorectal and pancreatic xenografts, resulting in striking increases in median survival. MTX-531 is exceptionally well tolerated in mice and uniquely does not lead to hyperglycemia and hyperinsulinemia commonly seen with predecessor pan PI3K inhibitors. MTX-531 acts as an agonist of PPARγ, a structural feature of the molecule that is thought to mitigate hyperglycemia induced by PI3K inhibition. This unique attribute of MTX-531 confers a favorable therapeutic index not typically seen with PI3K inhibitors. To the best of our knowledge, MTX-531 is the first reported pan-PI3K inhibitor that does not lead to hyperglycemia. The pharmaceutical profile of MTX-531 includes favorable cross-species oral bioavailability, microsomal stability, and a facile 3 step chemical synthesis. MTX-531, which has the unique capability of concurrently and selectively inhibiting PI3K and EGFR, illustrates the power of rational computational drug design to target multiple adaptive resistance mechanisms in a single molecule. The versatility of MTX-531 in both the single agent and combination settings offers a breadth of development strategies that continue to evolve as new combination candidates become available. MTX-531 is currently undergoing advanced preclinical development for anticipated first in human clinical trials in late 2024. Citation Format: Christopher E. Whitehead, Elizabeth K. Ziemke, Christy L. Frankowski-McGregor, Rachel A. Mumby, June Chung, Jinju Li, Nathaniel Osher, Oluwadara Coker, Michelle Norris, Scott Kopetz, Veera Baladandayuthapani, Melinda Hollingshead, Sharad Verma, Judith S. Sebolt-Leopold. MTX-531, a first-in-class pan-PI3K inhibitor spares hyperinsulinemia yielding durable tumor regressions and resilience to adaptive resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1230.

Abstract 718: CCR8 antibody drug conjugates: Targeting regulatory T cells for tumor sensitization

Abstract Background: Regulatory T (Treg) cells in the tumor microenvironment have an immune suppressive function, and their presence is associated with poor prognosis. Depletion of Treg cells may be a mechanism to sensitize tumors and represents a novel strategy for cancer immunotherapy. High expression of chemokine receptor CCR8 has been found in Treg cells in microenvironments of numerous tumors but not on Treg cells in systemic lymphoid tissues. The ability to selectively kill Treg cells in tumor environments may provide an opportunity for therapy that leaves Treg function intact elsewhere in the body where they normally mediate tolerance to self-antigen. Methods: We sought to identify CCR8 antibodies for therapeutics and designed an antibody discovery strategy to address the challenges of this target. CCR8 is a member of the G protein-coupled receptor (GPCR) family. Like many GPCRs, CCR8 is a valuable therapeutic antibody target but challenging to access due to its poor expression, membrane-dependent structure, and poor immunogenicity due to sequence conservation. We developed an antibody discovery platform (MPS) that specifically addresses each of these challenges through use of advanced immunization techniques and evolutionarily divergent host species (chickens) for robust immune responses against conserved targets. We extensively engineered CCR8 antigen to enable high expression for immunization. When sufficient antibody diversity was not obtained using our standard immunization techniques, we developed mRNA immunization techniques for this program. Antibody binding was measured using flow cytometry on transfected cells and human Treg cells. The ability of antibodies to inhibit CCR8 function was measured using intracellular calcium influx assays. Antibody internalization was measured using dye uptake assays and flow cytometry. Antibodies were conjugated with cytotoxic payloads and tested for the ability to mediate killing. Results: Using these approaches, we identified a panel of high-affinity antibodies that bound in the nanomolar or subnanomolar range with high specificity, and we selected a lead molecule to progress. We will present data from our antibody discovery campaign including mRNA immunization, binding profiles, GPCR functional data, receptor-mediated internalization, and the ability of antibody-drug conjugates (ADC) to kill CCR8+ cells, including human Treg cells, in vitro. Conclusion: Treg cells are a primary driver of the immunosuppressive microenvironment in many solid tumors. Targeting immune-suppressive CCR8+ Treg cells using ADC has potential to expand the treatment of solid tumors Citation Format: Lewis J. Stafford, Hayley Roth, Sarah Campbell, Samantha Brady, Valerie Fiers, FeiFan Yu, Andrew Tsourkas, Riley Payne, Meghan Pitts, Kyle Guldner, Tim Phillips, Breanna Tyrell, Colleen Ulke, Allison Snyder, Marianne Assogba, Holden Ohl, Ileine Sanchez, Benjamin Doranz, Joseph Rucker, Ross Chambers. CCR8 antibody drug conjugates: Targeting regulatory T cells for tumor sensitization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 718.

Uncovering the potentiality of quinazoline derivatives against Pseudomonas aeruginosa with antimicrobial synergy and SAR analysis.

Antimicrobial resistance has emerged as a covert global health crisis, posing a significant threat to humanity. If left unaddressed, it is poised to become the foremost cause of mortality worldwide. Among the multitude of resistant bacterial pathogens, Pseudomonas aeruginosa, a Gram-negative, facultative bacterium, has been responsible for mild to deadly infections. It is now enlisted as a global critical priority pathogen by WHO. Urgent measures are required to combat this formidable pathogen, necessitating the development of novel anti-pseudomonal drugs. To confront this pressing issue, we conducted an extensive screening of 3561 compounds from the ChemDiv library, resulting in the discovery of potent anti-pseudomonal quinazoline derivatives. Among the identified compounds, IDD-8E has emerged as a lead molecule, exhibiting exceptional efficacy against P. aeruginosa while displaying no cytotoxicity. Moreover, IDD-8E demonstrated significant pseudomonal killing, disruption of pseudomonal biofilm and other anti-bacterial properties comparable to a well-known antibiotic rifampicin. Additionally, IDD-8E's synergy with different antibiotics further strengthens its potential as a powerful anti-pseudomonal agent. IDD-8E also exhibited significant antimicrobial efficacy against other ESKAPE pathogens. Moreover, we elucidated the Structure-Activity-Relationship(SAR) of IDD-8E targeting the essential WaaP protein in P. aeruginosa. Altogether, our findings emphasize the promise of IDD-8E as a clinical candidate for novel anti-pseudomonal drugs, offering hope in the battle against antibiotic resistance and its devastating impact on global health.

Targeting human progesterone receptor (PR), through pharmacophore-based screening and molecular simulation revealed potent inhibitors against breast cancer

Breast cancer, the prevailing malignant tumor among women, is linked to progesterone and its receptor (PR) in both tumorigenesis and treatment responsiveness. Despite thorough investigation, the precise molecular mechanisms of progesterone in breast cancer remain unclear. The human progesterone receptor (PR) serves as an essential therapeutic target for breast cancer treatment, warranting the rapid design of small molecule therapeutics that can effectively inhibit HPR. By employing cutting-edge computational techniques like molecular screening, simulation, and free energy calculation, the process of identifying potential lead molecules from natural products has been significantly expedited. In this study, we employed pharmacophore-based virtual screening and molecular simulations to identify natural product-based inhibitors of human progesterone receptor (PR) in breast cancer treatment. High-throughput molecular screening of traditional Chinese medicine (TCM) and zinc databases was performed, leading to the identification of potential lead compounds. The analysis of binding modes for the top five compounds from both database provides valuable structural insights into the inhibition of HPR for breast cancer treatment. The top five hits exhibited enhanced stability and compactness compared to the reference compound. In conclusion, our study provides valuable insights for identifying and refining lead compounds as HPR inhibitors.

Identification and Development of Cyclic Peptide Inhibitors of Hypoxia Inducible Factors 1 and 2 That Disrupt Hypoxia-Response Signaling in Cancer Cells.

Hypoxia inducible factor (HIF) is a heterodimeric transcription factor composed of an oxygen-regulated α subunit and a constitutively expressed β subunit that serves as the master regulator of the cellular response to low oxygen concentrations. The HIF transcription factor senses and responds to hypoxia by significantly altering transcription and reprogramming cells to enable adaptation to a hypoxic microenvironment. Given the central role played by HIF in the survival and growth of tumors in hypoxia, inhibition of this transcription factor serves as a potential therapeutic approach for treating a variety of cancers. Here, we report the identification, optimization, and characterization of a series of cyclic peptides that disrupt the function of HIF-1 and HIF-2 transcription factors by inhibiting the interaction of both HIF-1α and HIF-2α with HIF-1β. These compounds are shown to bind to HIF-α and disrupt the protein-protein interaction between the α and β subunits of the transcription factor, resulting in disruption of hypoxia-response signaling by our lead molecule in several cancer cell lines.

Design, synthesis of new 2,4-thiazolidinediones: In-silico, in-vivo anti-diabetic and anti-inflammatory evaluation

In this study, a series of nine novel heterocyclic compounds were synthesized through a concise three-step reaction process. The synthesis involved Knoevenagel condensation at the 5th position of the 2,4-thiazolidinedione or rhodanine ring-system. Comprehensive physicochemical and spectral analyses, including FTIR, Mass, 1H NMR and 13C NMR, were performed to characterize the synthesized compounds. The synthesized derivatives were subjected to evaluation for their potential in various therapeutic domains. In-vivo anti-diabetic activity was assessed diabetes induced wistar rats, anti-inflammatory effects were gauged using the carrageenan and formalin induced rat paw edema model. Additionally, the in-vitro PPAR-γ modulatory activity, glucose uptake by using Saccharomyces cerevisiae and rat hemidiaphragm and cyclooxygenase inhibitory activity along with scavenge free radicals was tested by FRAP and DPPH method. According to the potential binding patterns of the most potent anti-diabetic compounds, namely 7a and 13a with the active sites of target PPAR-γ (PDB ID: 5U5L), was obtained through molecular docking using Schrodinger’s Glide model. Among the tested compounds, the compound 13a demonstrated significant antidiabetic activity with reduction in blood glucose levels (108.5 ± 2.171 mg/dL), comparable to the effect of pioglitazone (101.66 ± 0.95 mg/dL), similarly anti-inflammatory activity at fourth hour paw volume 93.6% and thickness at 3.99 ± 0.076 mm, respectively closer to that of standard drug diclofenac sodium (91.2% and 4.7 ± 0.057 mm) in carrageenan-induced paw edema in rat. The compound 13a displayed promising COX-2 inhibitory activity (IC50 = 7.82 μM) and DPPH antioxidant activity showcasing its multifaceted therapeutic potential. This study not only presents multi-targeting approach and highlights the significant potential compounds as a lead molecule for further therapeutic development.

Microbial lipopeptides: their pharmaceutical and biotechnological potential, applications, and way forward.

As lead molecules, cyclic lipopeptides with antibacterial, antifungal, and antiviral properties have garnered a lot of attention in recent years. Because of their potential, cyclic lipopeptides have earned recognition as a significant class of antimicrobial compounds with applications in pharmacology and biotechnology. These lipopeptides, often with biosurfactant properties, are amphiphilic, consisting of a hydrophilic moiety, like a carboxyl group, peptide backbone, or carbohydrates, and a hydrophobic moiety, mostly a fatty acid. Besides, several lipopeptides also have cationic groups that play an important role in biological activities. Antimicrobial lipopeptides can be considered as possible substitutes for antibiotics that are conventional to address the current drug-resistant issues as pharmaceutical industries modify the parent antibiotic molecules to render them more effective against antibiotic-resistant bacteria and fungi, leading to the development of more resistant microbial strains. Bacillus species produce lipopeptides, which are secondary metabolites that are amphiphilic and are typically synthesized by non-ribosomal peptide synthetases (NRPSs). They have been identified as potential biocontrol agents as they exhibit a broad spectrum of antimicrobial activity. A further benefit of lipopeptides is that they can be produced and purified biotechnologically or biochemically in a sustainable manner using readily available, affordable, renewable sources without harming the environment. In this review, we discuss the biochemical and functional characterization of antifungal lipopeptides, as well as their various modes of action, method of production and purification (in brief), and potential applications as novel antibiotic agents.

Experimental and Computational Methods to Assess Central Nervous System Penetration of Small Molecules.

In CNS drug discovery, the estimation of brain exposure to lead compounds is critical for their optimization. Compounds need to cross the blood-brain barrier (BBB) to reach the pharmacological targets in the CNS. The BBB is a complex system involving passive and active mechanisms of transport and efflux transporters such as P-glycoproteins (P-gp) and breast cancer resistance protein (BCRP), which play an essential role in CNS penetration of small molecules. Several in vivo, in vitro, and in silico methods are available to estimate human brain penetration. Preclinical species are used as in vivo models to understand unbound brain exposure by deriving the Kp,uu parameter and the brain/plasma ratio of exposure corrected with the plasma and brain free fraction. The MDCK-mdr1 (Madin Darby canine kidney cells transfected with the MDR1 gene encoding for the human P-gp) assay is the commonly used in vitro assay to estimate compound permeability and human efflux. The in silico methods to predict brain exposure, such as CNS MPO, CNS BBB scores, and various machine learning models, help save costs and speed up compound discovery and optimization at all stages. These methods enable the screening of virtual compounds, building of a CNS penetrable compounds library, and optimization of lead molecules for CNS penetration. Therefore, it is crucial to understand the reliability and ability of these methods to predict CNS penetration. We review the in silico, in vitro, and in vivo data and their correlation with each other, as well as assess published experimental and computational approaches to predict the BBB penetrability of compounds.

Untargeted metabolomics-based identification of bioactive compounds from Mangifera indica L. seed extracts in drug discovery through molecular docking and assessment of their anticancer potential.

Mangifera indica L. (mango), a medicinal plant rich in biologically active compounds, has potential to be used in disease-preventing and health-promoting products. The present investigation reveals and uncovers bioactive metabolites with remarkable therapeutic efficiency from mango (family: Anacardiaceae) seeds. Biological activity was determined by antimicrobial, antioxidant and anticancer assays, and metabolite profiling was performed on gas chromatography coupled to quadrupole time-of-flight mass spectrometry (GC-QTOF-MS) and liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) platforms. Validation of active metabolites was carried out by in silico molecular docking (Molinspiration Cheminformatics Server and PASS). Extracted and identified metabolites were screened; 54 compounds associated with various groups were selected for the in silico interaction study. Molecular docking revealed lead molecules with a potential binding energy score, efficacy and stable modulation with a selected protein domain. Investigation, directed by in vitro and in silico analysis, confirms mango seeds as an excellent source of potential metabolites as a therapeutic agent. © 2024 Society of Chemical Industry.

Synthesis of Novel Acetyl-11-keto-β-boswellic Acid Derivatives as Potential Anti-GBM Agents.

Acetyl-11-keto-β-boswellic acid (AKBA) is known to inhibit the growth of glioblastoma (GBM) cells and subcutaneous GBM. A series of acetyl-11-keto-β-boswellic acid (AKBA) derivatives containing the oxime-ester functionality or amide side chains were synthesized, and their anti-GBM activities were evaluated. Some of these compounds exhibited significant inhibitory activity against cell proliferation in U87 and U251 GBM cell lines, with IC50 values in the micromolar concentration range. Cellular thermal shift analysis showed that A-01 and A-10 improved the thermal stability of FOXM1, indicating that these highly active compounds may directly bind to FOXM1 in cells. Docking studies of the two most active compounds, A-01 and A-10, revealed key interactions between these compounds and the active site of FOXM1, in which the amide moiety at the C-24 position was essential for improving the activity. These results suggested that A-10 is a suitable lead molecule for the development of FOXM1 inhibitors. Thus, the rational design of AKBA derivatives with amide side chains holds significant potential for discovering of a new class of triterpenoids capable of inhibiting GBM cell proliferation.