Letters in Drug Design & Discovery最新文献

{"title":"Ligand-based Molecular Modeling of HDL Receptor SR-BI Inhibitors As Potent Anti-Hyperlipidemic Agents","authors":"Swati Verma, Sarvesh Paliwal","doi":"10.2174/0115701808239749230921113101","DOIUrl":"https://doi.org/10.2174/0115701808239749230921113101","url":null,"abstract":"Introduction:: The High-density lipoprotein (HDL) receptor, Scavenger receptor class B, type I (SRBI) plays a crucial role in lipoprotein metabolism, cholesterol homeostasis, and atherosclerosis. In the present study, a quantitative structure-activity relationship study (QSAR) investigation was conducted on a data set of 31 novel indolinyl thiazole-based inhibitors of SR-BI mediated lipid uptake. Method:: To build the QSAR model, Multiple linear regression analysis (MLR), partial least square analysis (PLS), and neural analysis (NN) were performed which were further evaluated internally as well as externally for the prediction of activity. The best QSAR model for MLR was selected with a correlation coefficient (r2) of 0.937, cross-validation r2cv of 0.908, and a standard error (S) value of 0.253. For PLS, r2 was 0.937 and for FFNN r2 was 0.961 (for the training set). This was further evaluated externally by a test set having r2 values 0.870 (MLR), 0.863(PLS), and 0.933(neural network) analysis. Result:: The final model comprised hydrophobic parameters (Lipole Z component) and steric parameters (molar refractivity and K alpha2 index). Conclusion:: All these descriptors generated comparable results which prove that the model generated is sound and has good predictability.","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis, Antiproliferative Evaluation, and Molecular Docking of Thieno[3,2-e]indazole Derivatives","authors":"Rafat M. Mohareb, Ibram Refat Mikhail, Marwa Soliman Gamaan, Ensaf S. Alwan","doi":"10.2174/0115701808287763240302165049","DOIUrl":"https://doi.org/10.2174/0115701808287763240302165049","url":null,"abstract":"Background: Although indazole derivatives are rare and may not be available easily in nature, there are many reports demonstrating their pharmaceutical and other applications. Objective: This study aimed to synthesize new indazole derivatives and evaluate their antiproliferative activity to produce new anti-cancer agents. Method: The 2-aryllidenecyclohexane-1,3-dione derivatives 3a-c were obtained through the reaction of cyclohexane-1,3-dione with aromatic aldehydes used for the synthesis of thieno-[3,2-e]indazole derivatives. These derivatives were characterized by extensive analytical and spectral studies and were further used as starting materials for some heterocyclic transformations to produce biologically active compounds. The antiproliferative activities of the newly synthesized compounds were evaluated against the six cancer cell lines, A549, HT-29, MKN-45, U87MG, SMMC-7721, and H460. Most of the tested compounds exhibited high cytotoxicity except a few compounds. Results: In this study, new compounds were synthesized, characterized, and evaluated toward the selected six cancer cell lines. All tested compounds displayed potent c-Met enzymatic activity with IC50 values ranging from 0.25 to 10.30 nM and potent prostate PC-3 cell line inhibition with IC50 values ranging from 0.17 to 9.31mM. Conclusion: The results obtained in this work demonstrated that the variations in substituents within the aryl moiety, together with the attached heterocyclic ring, have a notable influence on the antiproliferative activity. The results obtained in this work encourage further work in the future.","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Linear and Nonlinear QSAR Analysis of Benzimidazole Derivative XY123 in Prostate Cancer Treatment","authors":"Bing Li, Xiaoqiang Liu","doi":"10.2174/0115701808291381240226094729","DOIUrl":"https://doi.org/10.2174/0115701808291381240226094729","url":null,"abstract":"Background: Metastatic Castration-Resistant Prostate Cancer (mCRPC) represents a critical challenge in current prostate cancer treatment. Benzimidazole Derivative XY123 has emerged as a novel inhibitor for its treatment. Objective: This study aims to establish a robust Quantitative Structure-Activity Relationship (QSAR) model for predicting the activity of Benzimidazole Derivative XY123 derivatives, aiding the development of novel anti-prostate cancer drugs. Methods: Utilizing CODESSA software, descriptors were computed based on various moieties of Benzimidazole Derivative XY123 derivatives. Multiple linear regression models were constructed, and both linear and nonlinear QSAR models were developed using heuristics and gene expression programming. Results: The linear model with two descriptors demonstrated the best predictive capacity for inhibitor activity, while the nonlinear model generated through Gene Expression Programming (GEP) exhibited correlation coefficients of 0.83 and 0.82 for the training and test sets, respectively. The average errors were 0.03 and 0.05, indicating the stability and the improved predictive ability of the nonlinear model. Conclusion: The QSAR linear model has an advantage over the nonlinear model in optimizing Benzimidazole Derivative XY123, providing a direction for the development of effective drugs for mCRPC treatment.","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"WITHDRAWN: Therapeutic Effects of Cortex Phellodendri, Epimedium Brevicornu, and Earthworm on Chronic Prostatitis/Chronic Pelvic Pain Syndrome Mice","authors":"Muhammad Naveed, Sobia Noreen, Mohsin Khan, Muhammad Saeed, Xingxing Cui, Asadullah Madni, Zhou Xiaohui, Muhammad Furqan Akhtar","doi":"10.2174/0115701808240328231031103739","DOIUrl":"https://doi.org/10.2174/0115701808240328231031103739","url":null,"abstract":"The article has been withdrawn at the request of the authors of the journal Letters in Drug Design & Discovery. Bentham Science apologizes to the readers of the journal for any inconvenience this may have caused. The Bentham Editorial Policy on Article Withdrawal can be found at https://benthamscience.com/pages/editorial-policies-main BENTHAM SCIENCE DISCLAIMER: It is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere. Furthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained. Plagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered. By submitting a manuscript the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Deep Dive into PDE5 Inhibition: Innovative Discoveries via Virtual Screening","authors":"Abhijit Debnath, Hema Chaudhary, Parul Sharma, Rajesh Singh, Shikha Srivastava","doi":"10.2174/0115701808279586231221043744","DOIUrl":"https://doi.org/10.2174/0115701808279586231221043744","url":null,"abstract":"Background: PDE5 inhibitors have had a surge in popularity over the last decade owing to their efficacy in the treatment of erectile dysfunction, coronary vasculopathy, and pulmonary arterial hypertension. These inhibitors exhibit competitive binding with phosphodiesterase type 5 and inhibit the hydrolysis of cyclic guanosine monophosphate, hence elevating the levels of cGMP in smooth muscle cells and prolonging the duration of an erection. However, due to production costs and side effects, further research is needed to discover new PDE5 inhibitors. background: The field of PDE5 inhibitors has risen in popularity in the past decade because of the success of PDE5 inhibitors in treating erectile dysfunction. Due to the structural identity with cGMP; PDE5 inhibitors competitively bind with PDE5 and limit cGMP hydrolysis, which raises the cGMP level in smooth muscle cells and lengthens the duration of an erection. PDE5 inhibitors were also found to be beneficial for coronary vasculopathy, pulmonary arterial hypertension, and benign prostatic hyperplasia. But, due to the expensive cost of production and unwanted side effects, it is necessary to explore the possibility of the discovery of new PDE5 inhibitors. Objective: The study aimed to identify potent PDE5 inhibitors by employing the extensive application of computer-aided drug design. objective: To identify potent PDE5 inhibitors by employing the extensive application of computer-aided drug design. Method: Three different databases, named Million Molecules Database, Natural Product Database, and NCI Database, have been screened, which has been followed by filtering based on various druglikeness rules, docking, ADME, toxicity, consensus molecular docking, and 100 ns molecular dynamics simulation. method: Three different databases named Million Molecules Database, Natural Product Database, and NCI Database has been screened followed by filtering based on various drug-likeness such as Lipinski rule of five, Ghose rule, Veber rule, and Muegge rule, docking, ADME, toxicity, consensus molecular docking, and 100 ns Molecular dynamics simulation Results: Three compounds (ZINC05351336, ZINC12030898, and ZINC17949426) have exhibited stable-binding characteristics at the active site of PDE5, demonstrating a robust binding affinity. These molecules have been found to possess drug-like capabilities, effective ADME features, low toxicity, and high stability. Conclusion: The study has delved into the realm of PDE5 inhibitors, which have been found to be effective in treating erectile dysfunction, but high production costs and side effects necessitate new ones. Through computer-aided drug design and screening, three compounds have been identified with promising binding characteristics, drug-appropriate properties, effective ADME profiles, minimal toxicity, and stability, making them potential candidates for future PDE5 inhibitors","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring and Designing Potential Inhibitors of SIRT2 in Natural Products by Artificial Intelligence (AI) and Molecular Dynamics Methods","authors":"Yangyang Ni, Juxia Bai, Yuqi Zhang, Haoran Qiao, Liqun Liang, Junfeng Wan, Yanyan Zhu, Haijing Cao, Huiyu Li, Qingjie Zhao","doi":"10.2174/0115701808288696240308052948","DOIUrl":"https://doi.org/10.2174/0115701808288696240308052948","url":null,"abstract":"Background:: The histone deacetylase family of proteins, which includes the sirtuins, participates in a wide range of cellular processes, and is intimately involved in neurodegenerative illnesses. The research on sirtuins has garnered a lot of interest. However, there are currently no effective therapeutic drugs. Methods:: In order to explore the potential inhibitors of SIRTs, we first screened four potential lead compounds of SIRT2 in Traditional Chinese Medicine (TCM) for nervous disease using the Auto- Dock Vina method. Then, with Molecular Dynamics (MD) simulation method, we discovered how these inhibitors from Traditional Chinese herbal medicines affect this protein at the atomic level. Results and Discussion:: We found hydrophobic interactions between inhibitors and SIRT2 to be crucial. The small molecules have been found to have strong effect on the residues in the zincbinding domain, exhibiting relationship with the signaling pathway. Finally, based on the conformational characteristics and the MD properties of the four potential inhibitors in TCM, we have designed the new skeleton molecules according to the parameters of binding energy, fingerprint similarity, 3D similarity, and RO5, with AI method using MolAICal software. Conclusion:: We have proposed the candidate inhibitor of SIRT2. Our research has provided a new approach that can be used to explore potential inhibitors from TCM. This could potentially pave the way for the creation of effective medicines.","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140148183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fluconazole Microemulsions: Preparation, Statistical Optimization by Two-Level Factorial Design, and Physicochemical Evaluation","authors":"Payam Khazaeli, Abbas Pardakhty, Gholamreza Dehghannoudeh, Sina Safizade, Marzieh Sajadi Bami, Mandana Ohadi","doi":"10.2174/0115701808287346240228120148","DOIUrl":"https://doi.org/10.2174/0115701808287346240228120148","url":null,"abstract":"Background:: Candida albicans is the yeast that causes the fungal infection known as candidiasis. One of the standard methods for treating candida is the application of fluconazole. The low solubility of fluconazole in aqueous media is a big problem in the use of this agent. Novel drug delivery systems, such as microemulsions, could be applied to solve this problem. The main aim of this study was to perform statistical optimization of the formulation and physicochemical characterization of fluconazole microemulsion. Methods:: Optimization of the microemulsion formulation was done by using experimental design software, and then fluconazole was loaded onto the best formulation at a concentration of 1 % w/w. The physiochemistry of the microemulsion formulation was assessed by pH measurement, rheology measurement, simultaneous thermal analysis, and Scanning Electron Microscopy (SEM). Results:: The two-level fractional factorial design application demonstrated the optimum formulation to consist of surfactant, co-surfactant, oil content, and water, comprising 58%, 27%, 10%, and 5% of the formulation, respectively. Desirable thermal mass was observed up to 150°C. The formulation was a non-Newtonian shear-thinning liquid in terms of viscosity, with a reported pH between 6.5-7. Conclusion:: Considerably stable, high-quality microemulsion formulations containing fluconazole are presented, which are applicable for antifungal skin candidiasis treatment in clinical trials.","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140116463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anti-Tumor Activity of Indole: A Review","authors":"Momen R.F. Mohamed, Mai E. Shoman, Taha F. S. Ali, Gamal El-Din A. Abuo-Rahma","doi":"10.2174/0115701808288928240226104445","DOIUrl":"https://doi.org/10.2174/0115701808288928240226104445","url":null,"abstract":": Generally, heterocyclic compounds are included in a large class of pharmacologically active compounds. The indole scaffold in this category is widely distributed in nature and present in many active compounds, especially anti-cancer agents. Due to its unique physicochemical and biological properties, the indole platform has been considered a favorable scaffold in anti-cancer drug design and development. Various indole compounds (synthetic, semisynthetic, and natural) show remarkable anti-proliferative activity. According to the recent literature, this review describes the role of indole scaffolds as anti-cancer agents. Indole was reported to induce anti-tumor activity through multiple mechanisms, for example, Epidermal Growth Factor Receptors (EGFR), histone deacetylase (HDAC), kinase, DNA-topoisomerases, and tubulin inhibition. The current review focuses on some indole compounds with amazing effects against different types of cancers as there are too many FDA-approved drugs, for example, osimertinib, alectinib, and anlotinib in NSCLC treatment, panobinostat in multiple myeloma, midostaurin in acute myeloid leukemia treatment, etc. Moreover, several compounds are still in clinical trials to treat different cancer types. Additionally, there are some oxindole derivatives with potent inhibition against different types of tumors, such as ovarian cancer, colorectal cancer, and prostate cancer. Different series of oxindoles are promising and recommended for further studies due to their remarkable inhibition of tumor cells. Accordingly, the collection of data on a pharmacologically significant motif might aid researchers in further employing indoles in developing novel anti-cancer drugs with potentially fewer side effects and higher potency against this rapidly spreading disease.","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140106955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and Synthesis of Novel Anti-proliferative Formononetin Derivatives","authors":"Zeping Luo, Liwei Pan, XiuJu Yin, Hailin Chen","doi":"10.2174/0115701808278216231228045423","DOIUrl":"https://doi.org/10.2174/0115701808278216231228045423","url":null,"abstract":"aims: aimed to synthesize and evaluate the potential antineoplastic activity of eight newly synthesized FMN derivatives background: Formononetin (FMN) is an isoflavone component of the natural product Astragalus membranaceus. Its well-documented anticancer activity led to the synthesis of new derivatives. objective: This study aimed to synthesize and evaluate the potential antineoplastic activity of eight newly synthesized FMN derivatives. method: Evaluation of the anti-tumor effects and potential mechanisms of action of derivatives using methods such as tetrazolium bromidesalt (MTT), cell cloning, EdU staining, Tunel staining, Transwell chamber , flow cytometry, and enzyme-linked immunosorbent assay (ELISA). result: As indicated by the results, all compounds exhibited toxicity to all three types of cancer cells. Most derivatives exhibited more significant antiproliferative activity than FMN. In comparison with other derivatives, compound 8 displayed the maximum antiproliferative activity, with IC50 value of 8.973 ± 0.296, 7.240 ± 0.208, and 4.378 ± 0.380 μ mol/L for HeLa, A549, and HepG2 cells, separately. In addition, further experiments demonstrated that compound 8 could suppress in vitro proliferation of HepG2 cells, promote HepG2 cell apoptosis, suppress HepG2 cell migration and invasion, and arrest HepG2 cell growth in S phase. The mechanism may be through the reduction of Bcl-2 and Mcl-1 protein expression, the increase of Bax, P53, Fas, Caspase-3 and Caspase-9 protein expression, the reduction of mitochondrial membrane potential and the reduction of ATP production, thus promoting the apoptosis of HepG2 cells. conclusion: Compound 8 may serve as a lead compound with high potential in discovering novel antitumor drugs. Furthermore, it can be explored in depth as an anticancer drug. other: none","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140046494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"P-glycoproteins in the Pathology and Treatment of Alzheimer's Disease","authors":"Raghad H. Aljohani, Nouf F. Alruwali, Shorooq M. Alrashedi, Somaya M. Yousef, Shahad T. Alobaidan, Nehal M. Elsherbiny, Hebatallah H. Atteia","doi":"10.2174/0115701808293022240216070603","DOIUrl":"https://doi.org/10.2174/0115701808293022240216070603","url":null,"abstract":": Alzheimer's disease (AD), a central cause of dementia, is characterized by the accumulation of amyloid β- peptide (Aβ) peptides in the brain. P-glycoprotein (P-gp), a highly expressed protein in the BBB, plays a fundamental role in transporting Aβ from the brain to the blood and protecting the blood-brain barrier (BBB). The dysfunction or decreased abundance of this transporting protein is associated with the accumulation of Aβ, leading to dementia and cognitive deficits. In this review article, we consolidate the existing literature on the impact of P-gp in the pathophysiology and therapy of AD. Current evidence claims that p-gp is involved in AD pathology and that enhancing the activity of this transporter may be a promising therapeutic approach to hinder AD progression. There is also a growing interest in P-gp as a potential therapeutic target for AD. Hence, ongoing clinical trials and research should investigate P-gp inhibitor efficacy as a therapeutic approach for improving AD drug delivery to the brain and treatment outcomes.","PeriodicalId":18059,"journal":{"name":"Letters in Drug Design & Discovery","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140018047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}