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Journal articles on the topic 'Minimal pharmacophores'

Author: Grafiati

Published: 8 June 2024

Last updated: 31 July 2025

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1

Mortier, Jérémie, Pratik Dhakal, and Andrea Volkamer. "Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces." Molecules 23, no. 8 (2018): 1959. http://dx.doi.org/10.3390/molecules23081959.

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Pharmacophore models are an accurate and minimal tridimensional abstraction of intermolecular interactions between chemical structures, usually derived from a group of molecules or from a ligand-target complex. Only a limited amount of solutions exists to model comprehensive pharmacophores using the information of a particular target structure without knowledge of any binding ligand. In this work, an automated and customable tool for truly target-focused (T²F) pharmacophore modeling is introduced. Key molecular interaction fields of a macromolecular structure are calculated using the AutoGRID

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Petrikaite, Vilma, Eduardas Tarasevišius, and Alvydas Pavilonis. "New ethacridine derivatives as the potential antifungal and antibacterial preparations." Medicina 43, no. 8 (2007): 657. http://dx.doi.org/10.3390/medicina43080084.

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Until the 20th century fungal infections were rather easy cured, and the need of new antifungal drugs was low. However, low choice of antifungal preparations, their toxicity, limited spectrum of action, and ability to produce resistant strains show the need of new effective medicines for systemic fungal diseases in nowadays. Our goal of research was to synthesize new antimicrobial compounds containing three or more pharmacophores in one molecule. The initial 5-substituted-2-methylmercaptothiazolidin-4-ones were subjected to S-demethylation to yield 2- amino-substituted thiazolidinones. Ethacri

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Spasov, Alexander, Irina Ovchinnikova, Olga Fedorova, et al. "Amino Derivatives of Diaryl Pyrimidines and Azolopyrimidines as Protective Agents against LPS-Induced Acute Lung Injury." Molecules 28, no. 2 (2023): 741. http://dx.doi.org/10.3390/molecules28020741.

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The problem of lung damage originating from excessive inflammation and cytokine release during various types of infections remains relevant and stimulates the search for highly effective and safe drugs. The biological activity of the latter may be associated with the regulation of hyperactivation of certain immune cells and enzymes. Here, we propose the design and synthesis of amino derivatives of 4,6- and 5,7-diaryl substituted pyrimidines and [1,2,4]triazolo[1,5-a]pyrimidines as promising double-acting pharmacophores inhibiting IL-6 and NO. The anti-inflammatory activity of 14 target compoun

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Mishra, Pranjali, Muskan Srivastav, Yashveer Gautam, et al. "A REVIEW IN CURCUMINOIDS: CHEMISTRY, ANTICANCER ACTIVITY AND FUTURE PROSPECTS." INDIAN DRUGS 61, no. 05 (2024): 7–23. http://dx.doi.org/10.53879/id.61.05.14041.

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ABSTRACT Curcumin is a biologically active phytochemical which manifests therapeutic activities in numerous health conditions, including cancer. Several curcuminoids obtained naturally and synthesized artificially also showcase anti-cancer and anti-tumorigenic effects. However, its water insolubility poses difficulties in its application to biological systems, lowering its availability in living tissues, which can be overcome by using various micro-encapsulation and nano-formulations of curcumin. When used in combination with other chemotherapeutic drugs, curcumin enhances the anti-carcinogen

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Maatuf, Yossi, Matan Geron, and Avi Priel. "The Role of Toxins in the Pursuit for Novel Analgesics." Toxins 11, no. 2 (2019): 131. http://dx.doi.org/10.3390/toxins11020131.

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Chronic pain is a major medical issue which reduces the quality of life of millions and inflicts a significant burden on health authorities worldwide. Currently, management of chronic pain includes first-line pharmacological therapies that are inadequately effective, as in just a portion of patients pain relief is obtained. Furthermore, most analgesics in use produce severe or intolerable adverse effects that impose dose restrictions and reduce compliance. As the majority of analgesic agents act on the central nervous system (CNS), it is possible that blocking pain at its source by targeting n

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Wermelinger, Guilherme Freimann, Lucas Rubini, Anna Carolina Carvalho da Fonseca, et al. "A Novel MDM2-Binding Chalcone Induces Apoptosis of Oral Squamous Cell Carcinoma." Biomedicines 11, no. 6 (2023): 1711. http://dx.doi.org/10.3390/biomedicines11061711.

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Oral squamous cell carcinoma (OSCC) represents ~90% of all oral cancers, being the eighth most common cancer in men. The overall 5-year survival rate is only 39% for metastatic cancers, and currently used chemotherapeutics can cause important side effects. Thus, there is an urgency in developing new and effective anti-cancer agents. As both chalcones and 1,2,3-triazoles are valuable pharmacophores/privileged structures in the search for anticancer compounds, in this work, new 1,2,3-triazole-chalcone hybrids were synthesized and evaluated against oral squamous cell carcinoma. By using different

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Bourne, Yves, Gerlind Sulzenbacher, Laurent Chabaud, et al. "The Cyclic Imine Core Common to the Marine Macrocyclic Toxins Is Sufficient to Dictate Nicotinic Acetylcholine Receptor Antagonism." Marine Drugs 22, no. 4 (2024): 149. http://dx.doi.org/10.3390/md22040149.

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Macrocyclic imine phycotoxins are an emerging class of chemical compounds associated with harmful algal blooms and shellfish toxicity. Earlier binding and electrophysiology experiments on nAChR subtypes and their soluble AChBP surrogates evidenced common trends for substantial antagonism, binding affinities, and receptor-subtype selectivity. Earlier, complementary crystal structures of AChBP complexes showed that common determinants within the binding nest at each subunit interface confer high-affinity toxin binding, while distinctive determinants from the flexible loop C, and either capping t

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Caldas Lopes, Eloisi, Shieh Jae-Hung, Srikanth Ambati, et al. "Novel Alkylating Agent, Ureidomustine Exhibit Pre-Clinical Efficacy in B-Cell Lymphoma with Minimal Dose-Limiting Myelotoxicity." Blood 126, no. 23 (2015): 1556. http://dx.doi.org/10.1182/blood.v126.23.1556.1556.

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Abstract Many patients with B-cell lymphomas, including mantle cell lymphoma (MCL) and diffuse large B-cell lymphoma (DLBCL), are not cured by conventional chemo-immunotherapy. One reason for this is because these drugs, while effective, are limited by their narrow therapeutic window and significant toxicities. B-cell lymphomas are highly dependent on DNA damage checkpoints, and hence are biologically responsive to drugs that trigger these checkpoints. Hence, In order to identify superior DNA damaging anti-lymphoma drugs we evaluated a series of novel, third generation, DNA-directed alkylating

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Vawhal, Pallavi Kishor, Shailaja B. Jadhav, Sumit Kaushik, et al. "Coumarin-Based Sulfonamide Derivatives as Potential DPP-IV Inhibitors: Pre-ADME Analysis, Toxicity Profile, Computational Analysis, and In Vitro Enzyme Assay." Molecules 28, no. 3 (2023): 1004. http://dx.doi.org/10.3390/molecules28031004.

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Recent research on dipeptidyl peptidase-IV (DPP-IV) inhibitors has made it feasible to treat type 2 diabetes mellitus (T2DM) with minimal side effects. Therefore, in the present investigation, we aimed to discover and develop some coumarin-based sulphonamides as potential DPP-IV inhibitors in light of the fact that molecular hybridization of many bioactive pharmacophores frequently results in synergistic activity. Each of the proposed derivatives was subjected to an in silico virtual screening, and those that met all of the criteria and had a higher binding affinity with the DPP-IV enzyme were

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Robertson, Gregory T., Eric J. Bonventre, Timothy B. Doyle, et al. "In Vitro Evaluation of CBR-2092, a Novel Rifamycin-Quinolone Hybrid Antibiotic: Microbiology Profiling Studies with Staphylococci and Streptococci." Antimicrobial Agents and Chemotherapy 52, no. 7 (2008): 2324–34. http://dx.doi.org/10.1128/aac.01651-07.

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ABSTRACT We present data from antimicrobial assays performed in vitro that pertain to the potential clinical utility of a novel rifamycin-quinolone hybrid antibiotic, CBR-2092, for the treatment of infections mediated by gram-positive cocci. The MIC90s for CBR-2092 against 300 clinical isolates of staphylococci and streptococci ranged from 0.008 to 0.5 μg/ml. Against Staphylococcus aureus, CBR-2092 exhibited prolonged postantibiotic effects (PAEs) and sub-MIC effects (SMEs), with values of 3.2, 6.5, and >8.5 h determined for the PAE (3× MIC), SME (0.12× MIC), and PAE-SME (3× MIC/0.12× MIC)

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Alhadrami, Hani A., Ahmed M. Sayed, Heba Al-Khatabi, Nabil A. Alhakamy та Mostafa E. Rateb. "Scaffold Hopping of α-Rubromycin Enables Direct Access to FDA-Approved Cromoglicic Acid as a SARS-CoV-2 MPro Inhibitor". Pharmaceuticals 14, № 6 (2021): 541. http://dx.doi.org/10.3390/ph14060541.

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The COVID-19 pandemic is still active around the globe despite the newly introduced vaccines. Hence, finding effective medications or repurposing available ones could offer great help during this serious situation. During our anti-COVID-19 investigation of microbial natural products (MNPs), we came across α-rubromycin, an antibiotic derived from Streptomyces collinus ATCC19743, which was able to suppress the catalytic activity (IC50 = 5.4 µM and Ki = 3.22 µM) of one of the viral key enzymes (i.e., MPro). However, it showed high cytotoxicity toward normal human fibroblasts (CC50 = 16.7 µM). To

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Cheng, Jeffrey, Enming Xing, Shabber Mohammed, et al. "Abstract 3106: Design, synthesis, and screening of niclosamide analogs as androgen receptor degraders for hepatocellular carcinoma." Cancer Research 83, no. 7_Supplement (2023): 3106. http://dx.doi.org/10.1158/1538-7445.am2023-3106.

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Abstract Hepatocellular Carcinoma (HCC) is the leading form of liver cancer, the 6th most common type, and the 4th leading cause of cancer death worldwide. Interestingly, HCC occurs two to four times more in males than females. A possible explanation for this sexual dimorphism is the implication of androgen and the Androgen Receptor (AR). However, previous clinical trials among HCC patients have shown no significant survival benefit after the administration of antiandrogen drugs (e.g. Enzalutamide) that block the Ligand-Binding Domain (LBD) of the Full-length Androgen Receptor (AR-FL). Instead

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Osborne, Joseph, Naveed Hassan Akhtar, Shankar Vallabhajosula, et al. "Tc-99m labeled small-molecule inhibitors of prostate-specific membrane antigen (PSMA): New molecular imaging probes to detect metastatic prostate adenocarcinoma (PC)." Journal of Clinical Oncology 30, no. 5_suppl (2012): 173. http://dx.doi.org/10.1200/jco.2012.30.5_suppl.173.

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173 Background: Sensitive and specific imaging remains a clinically-relevant problem for men with PC. PSMA is a well established target for imaging of PC with therapeutic implications. We have recently developed novel 99mTc-labeled small molecule inhibitors of the enzymatic domain of PSMA based on glutamate-urea-glutamate and glutamate-urea-lysine pharmacophores, and contain a bis-imidazole chelator to complex Tc-99m. Preclinical studies with PSMA positive LNCaP cells and xenografts demonstrate that 99mTc-MIP-1404 and 99mTc-MIP-1405 bind to PSMA with high affinity and localize in tumors rapidl

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Hall, Ronald G., Jotam Pasipanodya, William C. Putnam, et al. "1319. Pharmacokinetics of Ceftolozane/Tazobactam in Patients with Burns." Open Forum Infectious Diseases 7, Supplement_1 (2020): S670—S671. http://dx.doi.org/10.1093/ofid/ofaa439.1501.

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Abstract Background Antimicrobial dosing in moderate/severe burns patients is complicated due to the potential unpredictable hyperdynamic pathophysiologic states including 1) hypoproteinemia, 2) acute kidney injury and 3) onset of septicemia. Therefore, distribution assumptions about the population pharmacokinetic (PopPK) profiles of either endogenous or xenobiotic pharmacophores in this patient population can lead to biased parameter estimates. In order to prevent potential bias an agnostic nonparametric adaptive grid approach to describe ceftolozane/tazobactam (C/T) PopPK profiles in patient

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15

Schlitzer, Martin, Labaniel Rodriguez, and Peter F. Kador. "Synthesis of potential aldose reductase inhibitors based on minimal pharmacophore requirements." Journal of Pharmacy and Pharmacology 53, no. 6 (2001): 831–39. http://dx.doi.org/10.1211/0022357011776180.

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Papke, Roger L., Kinga Chojnacka та Nicole A. Horenstein. "The Minimal Pharmacophore for Silent Agonism of the α7 Nicotinic Acetylcholine Receptor". Journal of Pharmacology and Experimental Therapeutics 350, № 3 (2014): 665–80. http://dx.doi.org/10.1124/jpet.114.215236.

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17

Magnin, David R., Prakash C. Taunk, James G. Robertson, et al. "Seco-prolinenitrile inhibitors of dipeptidyl peptidase IV define minimal pharmacophore requirements at P1." Bioorganic & Medicinal Chemistry Letters 16, no. 6 (2006): 1731–34. http://dx.doi.org/10.1016/j.bmcl.2005.11.098.

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18

Johnston, Alexis, and Adegboyega K. Oyelere. "Abstract 4492: Deferiprone optimization for the treatment of triple-negative breast cancer." Cancer Research 84, no. 6_Supplement (2024): 4492. http://dx.doi.org/10.1158/1538-7445.am2024-4492.

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Abstract Triple-negative breast cancer (TNBC) is the leading cause of new cancer cases and the second leading cause of cancer deaths in American women disproportionately affecting Black and Hispanic women under 40. Currently, there is no targeted therapy for TNBC and treatment options to manage this lethal disease include surgery, adjuvant chemotherapy and radiotherapy. Among the chemotherapy agents, combination of the PARP inhibitors with DNA-damaging results in a more promising anti-tumor effect. A better understanding of TNBC etiology has aided in unraveling the roles of two additional cell

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19

Cruz, María del Carmen, María Salazar, Yésica Garciafigueroa та ін. "Hypolipidemic Activity of New Phenoxyacetic Derivatives Related to α-Asarone with Minimal Pharmacophore Features". Drug Development Research 60, № 3 (2003): 186–95. http://dx.doi.org/10.1002/ddr.10281.

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Pratap, Uday P., Michael Tidwell, Annabel Maciolek, et al. "Abstract 4310: Novel analogues of indanone and tetralone-keto oximes as potent estrogen receptor beta agonists for treating GBM." Cancer Research 85, no. 8_Supplement_1 (2025): 4310. https://doi.org/10.1158/1538-7445.am2025-4310.

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Abstract Background: Glioblastoma (GBM) is the most common and aggressive brain tumor, with a poor 5-year survival rate. Epidemiological studies suggest that estrogen receptor beta (ERb) may inhibit brain tumor growth, highlighting the potential therapeutic role of ERb. However, the lack of potent, selective, and brain-permeable ERb ligands has limited the clinical application of ERb-based therapies. We recently identified indanone and tetralone-keto oximes as promising ERb agonists. To further optimize these compounds, we employed a structure-based drug design strategy, utilizing existing X-r

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Bjij, Imane, Pritika Ramharack, Shama Khan, Driss Cherqaoui, and Mahmoud E. S. Soliman. "Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase through Target-Focused Modelling." Molecules 24, no. 17 (2019): 3125. http://dx.doi.org/10.3390/molecules24173125.

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The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the enzyme may be targeted both covalently and non-covalently, minimal studies provide effective inhibitors against it. Recently, research has focused on covalent inhibitors based on their characteristic, highly-selective warheads and ability to prevent drug resistance. This prompted us to screen for new covalent inhibitors of Nedd4-1 using a combination of computational approaches. However, this task proved challenging due to the limited number of electrophilic moieties availabl

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Wood, Daniel J., J. Daniel Lopez-Fernandez, Leanne E. Knight, et al. "FragLites—Minimal, Halogenated Fragments Displaying Pharmacophore Doublets. An Efficient Approach to Druggability Assessment and Hit Generation." Journal of Medicinal Chemistry 62, no. 7 (2019): 3741–52. http://dx.doi.org/10.1021/acs.jmedchem.9b00304.

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23

Ostash, Bohdan, Emma Doud, and Victor Fedorenko. "The molecular biology of moenomycins: towards novel antibiotics based on inhibition of bacterial peptidoglycan glycosyltransferases." Biological Chemistry 391, no. 5 (2010): 499–504. http://dx.doi.org/10.1515/bc.2010.053.

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AbstractMoenomycins are phosphoglycolipid antibiotics and the only known natural product inhibitors of peptidoglycan glycosytransferases (PGTs). Techniques that would allow facile diversification of the moenomycin structure would facilitate the development of novel antibiotics, which are urgently needed in the wake of multidrug resistant bacterial infections. The cloning and initial characterization of the moenomycin biosynthetic genes has already redefined the minimal moenomycin pharmacophore and now opens the door for the biocombinatorial generation of bioactive moenomycin fragments. Here, w

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Gozalbes, Rafael, Silvia Mosulén, Rodrigo J. Carbajo, and Antonio Pineda-Lucena. "Development and NMR validation of minimal pharmacophore hypotheses for the generation of fragment libraries enriched in heparanase inhibitors." Journal of Computer-Aided Molecular Design 23, no. 8 (2009): 555–69. http://dx.doi.org/10.1007/s10822-009-9269-0.

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Ladouceur, Gaétan, Dale E. Mais, Joseph A. Jakubowski, Barbara G. Utterback, and David W. Robertson. "Structural homologies among thromboxane (TXA2) receptor antagonists: Minimal pharmacophoric requirements for high affinity interaction with TXA2 receptors." Bioorganic & Medicinal Chemistry Letters 1, no. 3 (1991): 173–78. http://dx.doi.org/10.1016/s0960-894x(01)80794-0.

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Mittal, Ravi K., and Priyank Purohit. "Quinoline-3-carboxylate Derivatives: A New Hope as an Antiproliferative Agent." Anti-Cancer Agents in Medicinal Chemistry 20, no. 16 (2020): 1981–91. http://dx.doi.org/10.2174/1871520620666200619175906.

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Background: The quinoline scaffold has been an attraction due to its pharmacological activities such as anti-HIV, anti-neoplastic, anti-asthmatic, anti-tuberculotic, anti-fungal, and anti-bacterial. Objective: The designed quinoline-3-carboxylate derivatives were synthesized through a two-step reaction and evaluated for antiproliferative activity against MCF-7 and K562 cell lines. Methods: Synthesized compounds were characterized by modern analytical techniques like NMR, 2DNMR, mass, and IR. Moreover, the purity of compounds was analyzed through the HPLC. In the progress of biological results,

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Khomutov, Maxim A., Fabio Giovannercole, Laura Onillon, et al. "A Desmethylphosphinothricin Dipeptide Derivative Effectively Inhibits Escherichia coli and Bacillus subtilis Growth." Biomolecules 13, no. 10 (2023): 1451. http://dx.doi.org/10.3390/biom13101451.

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New antibiotics are unquestionably needed to fight the emergence and spread of multidrug-resistant bacteria. To date, antibiotics targeting bacterial central metabolism have been poorly investigated. By determining the minimal inhibitory concentration (MIC) of desmethylphosphinothricin (Glu-γ-PH), an analogue of glutamate with a phosphinic moiety replacing the γ-carboxyl group, we previously showed its promising antibacterial activity on Escherichia coli. Herein, we synthetized and determined the growth inhibition exerted on E. coli by an L-Leu dipeptide derivative of Glu-γ-PH (L-Leu-D,L-Glu-γ

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Demeter, David A., Herschel J. R. Weintraub, and James J. Knittel. "The Local Minima Method (LMM) of Pharmacophore Determination: A Protocol for Predicting the Bioactive Conformation of Small, Conformationally Flexible Molecules." Journal of Chemical Information and Computer Sciences 38, no. 6 (1998): 1125–36. http://dx.doi.org/10.1021/ci980404z.

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Ji, Haitao, Benjamin Z. Stanton, Jotaro Igarashi, et al. "Minimal Pharmacophoric Elements and Fragment Hopping, an Approach Directed at Molecular Diversity and Isozyme Selectivity. Design of Selective Neuronal Nitric Oxide Synthase Inhibitors." Journal of the American Chemical Society 130, no. 12 (2008): 3900–3914. http://dx.doi.org/10.1021/ja0772041.

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Rasaeifar, Bahareh, Patricia Gomez-Gutierrez, and Juan J. Perez. "New Insights into the Stereochemical Requirements of the Bombesin BB1 Receptor Antagonists Binding." Pharmaceuticals 13, no. 8 (2020): 197. http://dx.doi.org/10.3390/ph13080197.

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Members of the family of bombesinlike peptides exert a wide range of biological activities both at the central nervous system and in peripheral tissues through at least three G-Protein Coupled Receptors: BB1, BB2 and BB3. Despite the number of peptide ligands already described, only a few small molecule binders have been disclosed so far, hampering a deeper understanding of their pharmacology. In order to have a deeper understanding of the stereochemical features characterizing binding to the BB1 receptor, we performed the molecular modeling study consisting of the construction of a 3D model o

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Martinenghi, Laura Daniela, Rie Jønsson, Torben Lund, and Håvard Jenssen. "Isolation, Purification, and Antimicrobial Characterization of Cannabidiolic Acid and Cannabidiol from Cannabis sativa L." Biomolecules 10, no. 6 (2020): 900. http://dx.doi.org/10.3390/biom10060900.

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The emergence of multi-drug resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) causes a major threat to public health due to its limited therapeutic options. There is an urgent need for the development of new effective antimicrobial agents and alternative strategies that are effective against resistant bacteria. The parallel legalization of cannabis and its products has fueled research into its many therapeutic avenues in many countries around the world. This study aimed at the development of a reliable method for the extraction, purification, characterization, and q

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DIYAROVA, N. R., A. YU NIKOLAEV, O. M. LAVROVA, et al. "SYNTHESIS OF HYBRID COMPOUNDS BASED ON CARBOXYLIC ACID HYDRAZIDES AND SPATIALLY HINDERED PYROCATECHIN ALDEHYDES." Herald of Technological University 27, no. 8 (2024): 5–9. https://doi.org/10.55421/1998-7072_2024_27_8_5.

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Modern neuropsychopharmacology is in active search of effective neurotropic compounds with minimal side effects. Various approaches are used to create such substances, for example, the principle of hybrid structures, which is an important direction in the creation of new bioactive systems. This approach allows combining different pharmacophore groups in one molecular complex to achieve improved pharmacological properties - increased activity, broader spectrum of action, and reduced side effects. Organophosphorus compounds play an important role in various fields such as medicine, agriculture,

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Ezekiel, Olugbogi A., Arobadade A. Oluwaotbiloba, Balogun A. Samuel, et al. "Application of In-silico Methodologies in Exploring the Antagonistic Potential of Trigonella frenum-graecum on Cyclooxygenase-2 (Cox-2) in Cancer Treatment." IPS Journal of Molecular Docking Simulations 2, no. 1 (2023): 26–36. http://dx.doi.org/10.54117/ijmds.v2i1.20.

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Cancer is a disease in which abnormal cells divide uncontrollably and destroy body tissue. This research is dispensed utilizing in-silico drug design. Cyclooxygenase-2 (Cox-2) has been used as a target protein of the molecular docking study and fenugreek phytoconstituents obtained from PubChem were docked against Cox-2’s pocket (PDB ID: 5IKV). We used Maestro 12.8 and the Schrödinger Suite to conduct computer-based drug testing. To document compounds with the best inhibitory ability to act as cyclooxygenase antagonists in the treatment of cancer. Sixty (60) compounds described with fenugreek w

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Motsilanyane, Andrew Rabontsi, Zimbili Mkhize, and Sphelele Sosibo. "Computational Studies for Selected Medicinal Plants against Dolutegravir using Ligand Based Pharmacophore, Molecular Docking, ADMET Predictionsand Molecular Dynamics Simulation." Pakistan Journal of Medical and Health Sciences 16, no. 1 (2022): 927–36. http://dx.doi.org/10.53350/pjmhs22161927.

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Human immunodeficiency virus type 1 (HIV-1) is the causative agent for acquired immunodeficiency syndrome (AIDS). In 2020, South Africa recorded an estimated 8,2 million people living with HIV. This extensive figure is a red flag to the country, as it causes serious economic burden to its health care system. In the quest for finding a suitable inhibitor for HIV-1 protease, computer aided drug design (CADD) approachstands out to be one of the leading fields of study in pursuit of a new drug for HIV. The Lipinski rule of five was applied in screening the ninety-two plant extracts from Ocium sant

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Zapata-Acevedo, César A., and Paul L. A. Popelier. "The IQA Energy Partition in a Drug Design Setting: A Hepatitis C Virus RNA-Dependent RNA Polymerase (NS5B) Case Study." Pharmaceuticals 15, no. 10 (2022): 1237. http://dx.doi.org/10.3390/ph15101237.

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The interaction of the thumb site II of the NS5B protein of hepatitis C virus and a pair of drug candidates was studied using a topological energy decomposition method called interacting quantum atoms (IQA). The atomic energies were then processed by the relative energy gradient (REG) method, which extracts chemical insight by computation based on minimal assumptions. REG reveals the most important IQA energy contributions, by atom and energy type (electrostatics, sterics, and exchange–correlation), that are responsible for the behaviour of the whole system, systematically from a short-range l

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Ma’arif, Burhan, Faisal Akhmal Muslikh, Luqman Alfani Najib, Ria Ramadhani Dwi Atmaja, and Meilina Ratna Dianti. "In Silico Antiosteoporosis Activity of 96% Ethanol Extract of Chrysophyllum cainito L. Leaves." Proceedings of International Pharmacy Ulul Albab Conference and Seminar (PLANAR) 1 (December 5, 2021): 61. http://dx.doi.org/10.18860/planar.v1i0.1460.

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Estrogen deficiency causes various health problems in postmenopausal women, including osteoporosis. Phytoestrogens are emerging as potential estrogen alternatives with minimal side effects. This study aimed to predict the antiosteoporosis activity of the compounds from 96% ethanol extract of Chyrsophyllum cainito L. leaves through in silico study on 3OLS protein, an X-ray protein of ERβ. In silico analysis was carried out on the compounds from metabolite profiling results of 96% ethanol extract of C. cainito leaves from previous studies. The structure of compounds resulting from metabolite pro

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Egejuru, Winner Amaka, Abel Ujaigbe Egbemhenghe, Bamidele Samson Omotara, et al. "Computational Identification of YQG-Like Small-molecule Inhibitors Targeting TIM-3 for Cancer Immunotherapy." International Journal of Biochemistry Research & Review 34, no. 1 (2025): 134–52. https://doi.org/10.9734/ijbcrr/2025/v34i1955.

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Aims: To identify potential small-molecule inhibitors of T-cell immunoglobulin and mucin domain-3 (TIM-3) through computational approaches and evaluate their interactions, stability, and structural dynamics. Study Design: A computational drug discovery study utilizing virtual screening, molecular docking, and molecular dynamics simulations. Methodology: A pharmacophore/similarity search was conducted using the PUBCHEM database, followed by molecular docking simulations to identify compounds with favorable binding properties to TIM-3. Three top-performing compounds (CID_146311758-TIM3, CID_1646

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Sharif, Ehesan U., Dillon H. Miles, Brandon R. Rosen, et al. "Abstract PR001: Discovery of Etrumadenant, a first-in-class dual A2a and A2b adenosine receptor antagonist for cancer immunotherapy." Molecular Cancer Therapeutics 23, no. 12_Supplement (2024): PR001. https://doi.org/10.1158/1538-8514.cancerchem24-pr001.

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Abstract High levels of adenosine are generated in the tumor microenvironment (TME) by sequential hydrolysis of extracellular ATP by the ecto-nucleotidases CD39 (ATP→AMP) and CD73 (AMP→adenosine). Adenosine activates A2a and A2b adenosine receptors on immune cells, resulting in immunosuppression. Since A2aR is expressed by a variety of lymphocytes, the suppressive effects of adenosine on this cell type can be potentially reversed by blocking the A2aR. In contrast, myeloid cells that have comparable expression of A2aR and A2bR require dual A2a/bR blockade for full reversal of the immunosuppress

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Francesconi, Valeria, Elena Cichero, Evgeny V. Kanov, et al. "Novel 1-Amidino-4-Phenylpiperazines as Potent Agonists at Human TAAR1 Receptor: Rational Design, Synthesis, Biological Evaluation and Molecular Docking Studies." Pharmaceuticals 13, no. 11 (2020): 391. http://dx.doi.org/10.3390/ph13110391.

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Targeting trace amine-associated receptor 1 (TAAR1) receptor continues to offer an intriguing opportunity to develop innovative therapies in different pharmacological settings. Pursuing our endeavors in the search for effective and safe human TAAR1 (hTAAR1) ligands, we synthesized a new series of 1-amidino-4-phenylpiperazine derivatives (1–16) based on the application of a combined pharmacophore model/scaffold simplification strategy for an in-house series of biguanide-based TAAR1 agonists. Most of the novel compounds proved to be more effective than their prototypes, showing nanomolar EC50 va

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McBride, Molly J., Sarah R. Pope, Kai Hu, et al. "Structure and assembly of the diiron cofactor in the heme-oxygenase–like domain of the N-nitrosourea–producing enzyme SznF." Proceedings of the National Academy of Sciences 118, no. 4 (2021): e2015931118. http://dx.doi.org/10.1073/pnas.2015931118.

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In biosynthesis of the pancreatic cancer drug streptozotocin, the tridomain nonheme-iron oxygenase SznF hydroxylates Nδ and Nω′ of Nω-methyl-l-arginine before oxidatively rearranging the triply modified guanidine to the N-methyl-N-nitrosourea pharmacophore. A previously published structure visualized the monoiron cofactor in the enzyme’s C-terminal cupin domain, which promotes the final rearrangement, but exhibited disorder and minimal metal occupancy in the site of the proposed diiron cofactor in the N-hydroxylating heme-oxygenase–like (HO-like) central domain. We leveraged our recent observa

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Zhou, Heyang, Niao Yang, Wei Li, et al. "Exploration of Baicalein-Core Derivatives as Potent Antifungal Agents: SAR and Mechanism Insights." Molecules 28, no. 17 (2023): 6340. http://dx.doi.org/10.3390/molecules28176340.

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Baicalein (BE), the major component of Scutellaria Baicalensis, exhibited potently antifungal activity against drug-resistant Candida albicans, and strong inhibition on biofilm formation. Therefore, a series of baicalein-core derivatives were designed and synthesized to find more potent compounds and investigate structure–activity relationship (SAR) and mode of action (MoA). Results demonstrate that A4 and B5 exert a more potent antifungal effect (MIC80 = 0.125 μg/mL) than BE (MIC80 = 4 μg/mL) when used in combination with fluconazole (FLC), while the MIC80 of FLC dropped from 128 μg/mL to 1 μ

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Hasan, Md Rifat, Ahad Amer Alsaiari, Burhan Zain Fakhurji, et al. "Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process." Molecules 27, no. 13 (2022): 4169. http://dx.doi.org/10.3390/molecules27134169.

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The conventional drug discovery approach is an expensive and time-consuming process, but its limitations have been overcome with the help of mathematical modeling and computational drug design approaches. Previously, finding a small molecular candidate as a drug against a disease was very costly and required a long time to screen a compound against a specific target. The development of novel targets and small molecular candidates against different diseases including emerging and reemerging diseases remains a major concern and necessitates the development of novel therapeutic targets as well as

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Raghuvanshi, Rinky, and Sandip B. Bharate. "Preclinical and Clinical Studies on Bryostatins, A Class of Marine-Derived Protein Kinase C Modulators: A Mini-Review." Current Topics in Medicinal Chemistry 20, no. 12 (2020): 1124–35. http://dx.doi.org/10.2174/1568026620666200325110444.

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: Bryostatins are complex macrolactones isolated from marine organisms Bryozoan Bugula neritina. They are potent modulators of protein kinase C isozymes (PKCα: ki = 1.3-188 nM), and are one of the most extensively investigated marine natural products in clinical trials. Although ~21 natural bryostatins have been isolated, however only bryostatin-1 (1) has received much interest among medicinal chemists and clinicians. The structure-activity relationship of bryostatins has been well established, with the identification of key pharmacophoric features important for PKC modulation. The low natural

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Hao, Wenhui, Shiying Che, Jinsheng Li, et al. "Synthesis of Berberine and Canagliflozin Chimera and Investigation into New Antibacterial Activity and Mechanisms." Molecules 27, no. 9 (2022): 2948. http://dx.doi.org/10.3390/molecules27092948.

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Berberine is an isoquinoline alkaloid isolated from Chinese herbal medicines such as Coptis chinensis. It has many pharmacological actions, such as antibacterial, hypoglycemic, anti-inflammatory, and so on. However, due to the low lipophilicity of berberine, it is difficult to penetrate the bacterial cell membrane and also difficult to be absorbed orally and usually needs a relatively high dose to achieve the ideal effect. The purpose of this study is to transform the structure of berberine in order to improve the bioavailability of berberine and reduce the dosage. Moreover, we introduce a pha

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Ting, Jasmine U., Maria Carmen S. Tan, Vincent Antonio S. Ng, Stephani Joy Y. Macalino, Virgilio C. Linis та Glenn G. Oyong. "Molecular Simulations of Unexplored Philippine Plant Constituents on the Inhibition of the Proinflammatory Marker NF-κB p50 Subunit". Crystals 14, № 5 (2024): 438. http://dx.doi.org/10.3390/cryst14050438.

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Inflammation serves as a pivotal defense mechanism orchestrated by the innate immune system to safeguard cellular health against adversities. Nonetheless, dysregulated inflammatory responses can precipitate chronic inflammatory ailments, notably autoimmune disorders. Central to this process are various pathways, with studies highlighting the pivotal role of transcription factors within the nuclear factor-kappa B (NF-κB) signaling pathway in disease onset and progression. This study concentrates on the p50 homodimer protein, a key transcription factor pivotal for the expression of proinflammato

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Branco, Jessica R., Vanessa G. Oliveira, Amanda M. Esteves, et al. "A Novel Naphthotriazolyl-4-oxoquinoline Derivative that Selectively Controls Breast Cancer Cells Survival Through the Induction of Apoptosis." Current Topics in Medicinal Chemistry 18, no. 17 (2018): 1465–74. http://dx.doi.org/10.2174/1568026618666180821142458.

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Background: Breast cancer is a major cause of death among women worldwide. Treatment for breast cancer involves the surgical removal of cancer tissue, followed by chemotherapy. Although the treatment is efficient, especially when the cancer is detected early, recurrence is common and is often resistant to the previous treatment. Therefore, a constant search for efficient and novel drugs for the treatment of breast cancer is mandatory. Recently, triazole derivatives have shown promising effects against different types of cancer, revealing these molecules as putative anticancer drugs. Experiment

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Lomovskaya, Olga, Kirk J. Nelson та Debora Rubio-Aparicio. "727. Potency of the β-Lactamase Inhibitor QPX7728 Is Minimally Affected by KPC Mutations that Reduce Potency of Ceftazidime–Avibactam". Open Forum Infectious Diseases 6, Supplement_2 (2019): S326. http://dx.doi.org/10.1093/ofid/ofz360.795.

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Abstract Background In the United States, carbapenem-resistant Enterobacteriaceae (CRE) are mainly represented by KPC-producing strains and ceftazidime–avibactam (C/A) is increasingly used to treat infections caused by KPC-producers. C/A resistant (C/A-R) mutants with mutations in blaKPC can be isolated in vitro and were reported in patients treated with C/A. QPX7728 (QPX) is a new ultra-broad-spectrum β-lactamase inhibitor based on a cyclic boronic acid pharmacophore with a potent activity against serine and metallo-β-lactamases. QPX in combination with meropenem (MER), M/Q, or cefepime (FEP)

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Prochnau, Jack, Daisy Medina, Xena Huang, et al. "Abstract 6859: Targeting scaffold/matrix associated regions in pancreatic ductal adenocarcinoma." Cancer Research 85, no. 8_Supplement_1 (2025): 6859. https://doi.org/10.1158/1538-7445.am2025-6859.

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Abstract Pancreatic cancer is the tenth most common cancer in the United States and is projected to become the second leading cause of cancer-related death by 2030. Most cases arise in exocrine cells and are driven by genetic mutations, such as KRAS and CDKN2A, as well as modifiable risk factors, including alcohol use, chronic pancreatitis, and obesity. The aggressive nature of pancreatic ductal adenocarcinoma (PDAC), coupled with its complex tumor microenvironment, leads to late-stage diagnoses and a five-year survival rate of 13%. Despite advances in treatment, which include surgical resecti

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Sokolova, K. V., V. V. Stavytskyi, S. О. Konovalova, O. A. Podpletnya, S. I. Kovalenko, and A. P. Avdeenko. "Design and search for prospective diuretics (CA II Inhibitors) among aroylhydrazones of esters quinone oxime using in silico and in vivo methodology." Medicni perspektivi 27, no. 4 (2022): 27–37. http://dx.doi.org/10.26641/2307-0404.2022.4.271120.

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The design and search for new selective inhibitors of CA II with a better pharmacological profile, which would cause minimal electrolyte disturbances in the body, remains an urgent problem of medical chemistry and pharmacology today. It is important that the discovered new classes of inhibitors do not always contain the main “pharmacophoric” function (sulfamide), which is characteristic of “classic” drugs (Acetazolamide, Methazolamide, Ethoxzolamide, Dorzolamide and others), but are derivatives of phenols, polyamines, coumarins/thiocoumarins, ureas, thioureas, hydroxamates, etc. These molecule

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Sokolova, K.V., V.V. Stavytskyi, S.О. Konovalova, O.A. Podpletnya, S.I. Kovalenko, and A.P. Avdeenko. "Design and search for prospective diuretics (CA II Inhibitors) among aroylhydrazones of esters quinone oxime using in silico and in vivo methodology." Medicni perspektivi 27, no. 4 (2022): 27–37. https://doi.org/10.26641/2307-0404.2022.4.271120.

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The design and search for new selective inhibitors of CA II with a better pharmacological profile, which would cause minimal electrolyte disturbances in the body, remains an urgent problem of medical chemistry and pharmacology today. It is important that the discovered new classes of inhibitors do not always contain the main “pharmacophoric” function (sulfamide), which is characteristic of “classic” drugs (Acetazolamide, Methazolamide, Ethoxzolamide, Dorzolamide and others), but are derivatives of phenols, polyamines, coumarins/thiocoumarins, ureas, thioureas, hydr

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