keyword
https://read.qxmd.com/read/38386576/aegnn-m-a-3d-graph-spatial-co-representation-model-for-molecular-property-prediction
#21
JOURNAL ARTICLE
Lijun Cai, Yuling He, Xiangzheng Fu, Linlin Zhuo, Quan Zou, Xiaojun Yao
Improving the drug development process can expedite the introduction of more novel drugs that cater to the demands of precision medicine. Accurately predicting molecular properties remains a fundamental challenge in drug discovery and development. Currently, a plethora of computer-aided drug discovery (CADD) methods have been widely employed in the field of molecular prediction. However, most of these methods primarily analyze molecules using low-dimensional representations such as SMILES notations, molecular fingerprints, and molecular graph-based descriptors...
February 22, 2024: IEEE Journal of Biomedical and Health Informatics
https://read.qxmd.com/read/38385872/chemmort-an-automatic-admet-optimization-platform-using-deep-learning-and-multi-objective-particle-swarm-optimization
#22
JOURNAL ARTICLE
Jia-Cai Yi, Zi-Yi Yang, Wen-Tao Zhao, Zhi-Jiang Yang, Xiao-Chen Zhang, Cheng-Kun Wu, Ai-Ping Lu, Dong-Sheng Cao
Drug discovery and development constitute a laborious and costly undertaking. The success of a drug hinges not only good efficacy but also acceptable absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties. Overall, up to 50% of drug development failures have been contributed from undesirable ADMET profiles. As a multiple parameter objective, the optimization of the ADMET properties is extremely challenging owing to the vast chemical space and limited human expert knowledge. In this study, a freely available platform called Chemical Molecular Optimization, Representation and Translation (ChemMORT) is developed for the optimization of multiple ADMET endpoints without the loss of potency (https://cadd...
January 22, 2024: Briefings in Bioinformatics
https://read.qxmd.com/read/38374606/in-silico-drug-design-strategies-for-discovering-novel-tuberculosis-therapeutics
#23
REVIEW
Christian S Carnero Canales, Aline Renata Pavan, Jean Leandro Dos Santos, Fernando Rogério Pavan
INTRODUCTION: Tuberculosis remains a significant concern in global public health due to its intricate biology and propensity for developing antibiotic resistance. Discovering new drugs is a protracted and expensive endeavor, often spanning over a decade and incurring costs in the billions. However, computer-aided drug design (CADD) has surfaced as a nimbler and more cost-effective alternative. CADD tools enable us to decipher the interactions between therapeutic targets and novel drugs, making them invaluable in the quest for new tuberculosis treatments...
February 19, 2024: Expert Opinion on Drug Discovery
https://read.qxmd.com/read/38366974/graphlambda-fusion-graph-neural-networks-for-binding-affinity-prediction
#24
JOURNAL ARTICLE
Ghaith Mqawass, Petr Popov
Predicting the binding affinity of protein-ligand complexes is crucial for computer-aided drug discovery (CADD) and the identification of potential drug candidates. The deep learning-based scoring functions have emerged as promising predictors of binding constants. Building on recent advancements in graph neural networks, we present graphLambda for protein-ligand binding affinity prediction, which utilizes graph convolutional, attention, and isomorphism blocks to enhance the predictive capabilities. The graphLambda model exhibits superior performance across CASF16 and CSAR HiQ NRC benchmarks and demonstrates robustness with respect to different types of train-validation set partitions...
February 17, 2024: Journal of Chemical Information and Modeling
https://read.qxmd.com/read/38343400/unraveling-potential-glyoxalase-i-inhibitors-utilizing-structure-based-drug-design-techniques
#25
JOURNAL ARTICLE
Mohammad H Fetian, Qosay A Al-Balas
BACKGROUND: Glyoxalase system detoxifies methylglyoxal and other ketoaldehydes to produce innocuous metabolites that allow the cells to function normally. Its inhibition in cancer cells causes these toxic metabolites to accumulate, and the cancer cells enter the apoptotic stage. METHODS: The techniques of Computer-Aided Drug Design (CADD) were used, and the compounds possessing a zinc-binding group from commercial databases were extracted, using the pharmacophore search protocol...
2024: Advances and Applications in Bioinformatics and Chemistry: AABC
https://read.qxmd.com/read/38313945/targeted-drug-designing-for-treating-masticatory-myofascial-pain-dysfunction-syndrome-an-in-silico-simulation-study
#26
JOURNAL ARTICLE
Ramya Suresh, Ramya Ramadoss, Mukesh Doble, Karthikeyan Ramalingam, Sandhya Sundar, Suganya Panneer Selvam
Background Masticatory Myofascial Pain Dysfunction Syndrome (MMPDS) is a musculoligamentous disorder that shares similarities with temporomandibular joint pain and odontogenic pain. It manifests as dull or aching pain in masticatory muscles, influenced by jaw movement. Computer-aided drug design (CADD) encompasses various theoretical and computational approaches used in modern drug discovery. Molecular docking is a prominent method in CADD that facilitates the understanding of drug-bimolecular interactions for rational drug design, mechanistic studies & the formation of stable complexes with increased specificity and potential efficacy...
January 2024: Curēus
https://read.qxmd.com/read/38313820/whole-exome-sequencing-identifies-cancer-associated-variants-of-the-endo-lysosomal-ion-transport-channels-in-the-saudi-population
#27
JOURNAL ARTICLE
Lama Binobaid, Homood M As Sobeai, Khalid Alhazzani, Lama AlAbdi, Meshari M Alwazae, Moureq Alotaibi, John Parrington, Ali Alhoshani
BACKGROUND: Although national efforts are underway to document the genomic variability of the Saudi population relative to other populations, such variability remains largely unexplored. Genetic variability is known to impact the fate of cells and increase or decrease the risk of a variety of complex diseases including cancer forms. Therefore, the identification of variants associated with cancer susceptibility in Saudi population may protect individuals from cancer or aid in patient-tailored therapies...
March 2024: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
https://read.qxmd.com/read/38308532/an-interdisciplinary-course-on-computer-aided-drug-discovery-to-broaden-student-participation-in-original-scientific-research
#28
JOURNAL ARTICLE
Christopher Stratton, Avery Christensen, Chelsey Jordan, Brian A Salvatore, Elahe Mahdavian
We present a new highly interdisciplinary course in computer-aided drug discovery (CADD). This course was developed in response to a call for alternative pedagogical approaches during the COVID-19 pandemic, which caused the cancellation of a face-to-face summer research program sponsored by the Louisiana Louisiana Biomedical Research Network (LBRN). The course integrates guided research and educational experiences for chemistry, biology, and computer science students. We implement research-based methods with publicly available tools in bioinformatics and molecular modeling to identify and prioritize promising anti-viral drug candidates...
February 3, 2024: Biochemistry and Molecular Biology Education
https://read.qxmd.com/read/38299276/egfr-kinase-inhibiting-amino-enones-for-breast-cancer-cadd-approach
#29
JOURNAL ARTICLE
Deena Gladies Raymond Mohanraj, Manikandan Alagumuthu, Subha Chellam, Abishek Suresh Kumar, Tejaswini Nagaraj Poojari, Jeevitha Suresh Kumar, Palaniraja Subramaniam
BACKGROUND: The Computer-Aided Drug Discovery (CADD) approach was used to develop a few Epidermal Growth Factor Receptor (EGFR) kinase inhibitors. EGFR kinase expression is highly associated with genomic instability, higher proliferation, lower hormone receptor levels, and HER2 over-expression. It is more common in breast cancer. Thus, EGFR Kinase is one of the main targets in discovering new cancer medicine. OBJECTIVE: To computationally validate some amides substituted β-amino enones as EGFR inhibitors and to carry out associated in vitro anticancer agents...
January 30, 2024: Current Computer-aided Drug Design
https://read.qxmd.com/read/38281964/exploring-the-association-of-esr1-and-esr2-gene-snps-with-polycystic-ovary-syndrome-in-human-females-a-comprehensive-association-study
#30
JOURNAL ARTICLE
Fatima Muccee, Naeem Mahmood Ashraf, Suhail Razak, Tayyaba Afsar, Nadia Hussain, Fohad Mabood Husain, Huma Shafique
BACKGROUND: Polycystic Ovary Syndrome (PCOS) affects a significant proportion of human females worldwide and is characterized by hormonal, metabolic, and reproductive dysfunctions, including infertility, irregular menstrual cycles, acanthosis nigricans, and hirsutism. Mutations in the estrogen receptor genes ESR1 and ESR2, involved in normal follicular development and ovulation, can contribute to development of the PCOS. The present study focuses on investigating the potential correlation between single nucleotide polymorphisms (SNPs) of ESR1 and ESR2 genes and the incidence of this syndrome...
January 29, 2024: Journal of Ovarian Research
https://read.qxmd.com/read/38280992/compound-heterozygous-wnt10a-missense-variations-exacerbated-the-tooth-agenesis-caused-by-hypohidrotic-ectodermal-dysplasia
#31
JOURNAL ARTICLE
Yiting Liu, Jing Sun, Caiqi Zhang, Yi Wu, Siyuan Ma, Xuechun Li, Xiaoshan Wu, Qingping Gao
BACKGROUND: The aim of this study was to analyse the differences in the phenotypes of missing teeth between a pair of brothers with hypohidrotic ectodermal dysplasia (HED) and to investigate the underlying mechanism by comparing the mutated gene loci between the brothers with whole-exome sequencing. METHODS: The clinical data of the patients and their mother were collected, and genomic DNA was extracted from peripheral blood samples. By Whole-exome sequencing filtered for a minor allele frequency (MAF) ≤0...
January 27, 2024: BMC Oral Health
https://read.qxmd.com/read/38276629/lysine-specific-demethylase-1-inhibitors-a-comprehensive-review-utilizing-computer-aided-drug-design-technologies
#32
REVIEW
Di Han, Jiarui Lu, Baoyi Fan, Wenfeng Lu, Yiwei Xue, Meiting Wang, Taigang Liu, Shaoli Cui, Qinghe Gao, Yingchao Duan, Yongtao Xu
Lysine-specific demethylase 1 (LSD1/KDM1A) has emerged as a promising therapeutic target for treating various cancers (such as breast cancer, liver cancer, etc.) and other diseases (blood diseases, cardiovascular diseases, etc.), owing to its observed overexpression, thereby presenting significant opportunities in drug development. Since its discovery in 2004, extensive research has been conducted on LSD1 inhibitors, with notable contributions from computational approaches. This review systematically summarizes LSD1 inhibitors investigated through computer-aided drug design (CADD) technologies since 2010, showcasing a diverse range of chemical scaffolds, including phenelzine derivatives, tranylcypromine (abbreviated as TCP or 2-PCPA) derivatives, nitrogen-containing heterocyclic (pyridine, pyrimidine, azole, thieno[3,2-b]pyrrole, indole, quinoline and benzoxazole) derivatives, natural products (including sanguinarine, phenolic compounds and resveratrol derivatives, flavonoids and other natural products) and others (including thiourea compounds, Fenoldopam and Raloxifene, (4-cyanophenyl)glycine derivatives, propargylamine and benzohydrazide derivatives and inhibitors discovered through AI techniques)...
January 22, 2024: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://read.qxmd.com/read/38263521/optadmet-a-web-based-tool-for-substructure-modifications-to-improve-admet-properties-of-lead-compounds
#33
REVIEW
Jiacai Yi, Shaohua Shi, Li Fu, Ziyi Yang, Pengfei Nie, Aiping Lu, Chengkun Wu, Yafeng Deng, Changyu Hsieh, Xiangxiang Zeng, Tingjun Hou, Dongsheng Cao
Lead optimization is a crucial step in the drug discovery process, which aims to design potential drug candidates from biologically active hits. During lead optimization, active hits undergo modifications to improve their absorption, distribution, metabolism, excretion and toxicity (ADMET) profiles. Medicinal chemists face key questions regarding which compound(s) should be synthesized next and how to balance multiple ADMET properties. Reliable transformation rules from multiple experimental analyses are critical to improve this decision-making process...
January 23, 2024: Nature Protocols
https://read.qxmd.com/read/38263370/human-whole-exome-genotype-data-for-alzheimer-s-disease
#34
JOURNAL ARTICLE
Yuk Yee Leung, Adam C Naj, Yi-Fan Chou, Otto Valladares, Michael Schmidt, Kara Hamilton-Nelson, Nicholas Wheeler, Honghuang Lin, Prabhakaran Gangadharan, Liming Qu, Kaylyn Clark, Amanda B Kuzma, Wan-Ping Lee, Laura Cantwell, Heather Nicaretta, Jonathan Haines, Lindsay Farrer, Sudha Seshadri, Zoran Brkanac, Carlos Cruchaga, Margaret Pericak-Vance, Richard P Mayeux, William S Bush, Anita Destefano, Eden Martin, Gerard D Schellenberg, Li-San Wang
The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to a joint analysis. Here we present a bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced using ten capture kits in fourteen sequencing centers in the Alzheimer's Disease Sequencing Project. The joint-genotype called variant-called format (VCF) file contains only positions within the union of capture kits. The VCF was then processed specifically to account for the batch effects arising from the use of different capture kits from different studies...
January 23, 2024: Nature Communications
https://read.qxmd.com/read/38260445/enabling-systemic-identification-and-functionality-profiling-for-cdc42-homeostatic-modulators
#35
Satyaveni Malasala, Fereshteh Azimian, Yan-Hua Chen, Jeffery L Twiss, Christi Boykin, Shayan Nik Akhtar, Qun Lu
UNLABELLED: Homeostatic modulation is pivotal in modern therapeutics. However, the discovery of bioactive materials to achieve this functionality is often random and unpredictive. Here, we enabled a systemic identification and functional classification of chemicals that elicit homeostatic modulation of signaling through Cdc42, a classical small GTPase of Ras superfamily. Rationally designed for high throughput screening, the capture of homeostatic modulators (HMs) along with molecular re-docking uncovered at least five functionally distinct classes of small molecules...
January 8, 2024: bioRxiv
https://read.qxmd.com/read/38259032/broken-silence-22-841-predicted-deleterious-synonymous-variants-identified-in-the-human-exome-through-computational-analysis
#36
JOURNAL ARTICLE
Ana Carolina Mello, Delva Leao, Luis Dias, Felipe Colombelli, Mariana Recamonde-Mendoza, Andreia Carina Turchetto-Zolet, Ursula Matte
Synonymous single nucleotide variants (sSNVs) do not alter the primary structure of a protein, thus it was previously accepted that they were neutral. Recently, several studies demonstrated their significance to a range of diseases. Still, variant prioritization strategies lack focus on sSNVs. Here, we identified 22,841 deleterious synonymous variants in 125,748 human exomes using two in silico predictors (SilVA and CADD). While 98.2% of synonymous variants are classified as neutral, 1.8% are predicted to be deleterious, yielding an average of 9...
2024: Genetics and Molecular Biology
https://read.qxmd.com/read/38256856/computer-aided-drug-design-and-drug-discovery-a-prospective-analysis
#37
REVIEW
Sarfaraz K Niazi, Zamara Mariam
In the dynamic landscape of drug discovery, Computer-Aided Drug Design (CADD) emerges as a transformative force, bridging the realms of biology and technology. This paper overviews CADDs historical evolution, categorization into structure-based and ligand-based approaches, and its crucial role in rationalizing and expediting drug discovery. As CADD advances, incorporating diverse biological data and ensuring data privacy become paramount. Challenges persist, demanding the optimization of algorithms and robust ethical frameworks...
December 22, 2023: Pharmaceuticals
https://read.qxmd.com/read/38232131/discovery-of-n-1-6-oxo-1-6-dihydropyrimidine-pyrazole-acetamide-derivatives-as-novel-noncovalent-dpre1-inhibitors-against-mycobacterium-tuberculosis
#38
JOURNAL ARTICLE
Liu Yang, Xueping Hu, Yang Lu, Ruolan Xu, Yaping Xu, WanLi Ma, Md Shah Alam, Tianyu Zhang, Xin Chai, Yixuan Lei, Qing Ye, Xiaowu Dong, Yu Kang, Jinxin Che, Tingjun Hou, Dan Li
Decaprenylphosphoryl-β-d-ribose oxidase (DprE1) is a promising target for treating tuberculosis (TB). Currently, most novel DprE1 inhibitors are discovered through high-throughput screening, while computer-aided drug design (CADD) strategies are expected to promote the discovery process. In this study, with the aid of structure-based virtual screening and computationally guided design, a series of novel scaffold N -(1-(6-oxo-1,6-dihydropyrimidine)-pyrazole) acetamide derivatives with significant antimycobacterial activities were identified...
January 17, 2024: Journal of Medicinal Chemistry
https://read.qxmd.com/read/38217317/identification-characterization-and-cadd-analysis-of-plasmodium-dmap1-reveals-it-as-a-potential-molecular-target-for-new-anti-malarial-discovery
#39
JOURNAL ARTICLE
Merlyne Lawrence, Juhi Khurana, Ashish Gupta
Developing drug resistance in the malaria parasite is a reason for apprehension compelling the scientific community to focus on identifying new molecular targets that can be exploited for developing new anti-malarial compounds. Despite the availability of the Plasmodium genome, many protein-coding genes in Plasmodium are still not characterized or very less information is available about their functions. DMAP1 protein is known to be essential for growth and plays an important role in maintaining genomic integrity and transcriptional repression in vertebrate organisms...
January 12, 2024: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/38213241/caffeic-acid-3-4-dihydroxyphenethyl-ester-prevents-colorectal-cancer-through-inhibition-of-multiple-cancer-promoting-signal-pathways-in-1-2-dimethylhydrazine-dextran-sodium-sulphate-mouse-model
#40
JOURNAL ARTICLE
Jin Tao, Zhou Qian, Shen Jichen, Zhang Zhizhong, Lian Xiaoyuan
OBJECTIVE: To elucidate the potential feature and mechanism of the caffeic acid 3,4-dihydroxyphenethyl ester (CADPE) molecule, which can prevent colorectal cancer (CRC) in the 1,2-Dimethylhydrazine (DMH)/dextran sodium sulphate (DSS)-induced mouse model. METHODS: Institute of cancer research (ICR) male mice were injected with 20 mg/kg DMH for a week. After that, 2% DSS was administered in the drinking water for another 7 d. The CADPE treatment was given to the DMH/DSS induced male mice at three different periods until their sacrifice...
February 2024: Journal of Traditional Chinese Medicine
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