Article
Pharmacology & Pharmacy
Alejandro Valdes-Jimenez, Daniel Jimenez-Gonzalez, Aytug K. Kiper, Susanne Rinne, Niels Decher, Wendy Gonzalez, Miguel Reyes-Parada, Gabriel Nunez-Vivanco
Summary: Identifying similar three-dimensional amino acid patterns in different proteins can help explain the polypharmacological profile of drugs and facilitate the design of novel multitarget compounds. Most current computational tools only compare known binding sites and overlook other important 3D patterns. This study introduces Geomfinder 2.0, an improved algorithm for the exploration and discovery of similar and druggable 3D patterns. The new algorithm achieves significantly faster execution speed and allows for the comparison of quaternary structures.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemical Research Methods
A. K. M. Azad, Mojdeh Dinarvand, Alireza Nematollahi, Joshua Swift, Louise Lutze-Mann, Fatemeh Vafaee
Summary: Drug similarity studies aim to explore similar therapeutic actions among drugs, utilizing various sources of evidence to derive a multi-modal drug-drug similarity network. The resulting database, DrugSimDB, provides an exhaustive platform for identifying validated repositioning candidates and in-silico drug development applications.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Yao-Yu Hsieh, Jia-Ling Du, Pei-Ming Yang
Summary: By employing a gene expression-based drug repositioning strategy, this study identifies VU-0365114 as a novel type of tubulin inhibitor with broad-spectrum anticancer activity, especially in colorectal cancer cells. It is not limited by multidrug resistance proteins and does not exhibit significant off-target effects.
MOLECULAR ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sita Sirisha Madugula, Selvaraman Nagamani, Esther Jamir, Lipsa Priyadarsinee, G. Narahari Sastry
Summary: This study applied a polypharmacology guided computational drug repurposing approach to identify 34 drugs with predicted antitubercular and anti-mycobacterial activity, 21 of which are antibiotics and 4 are non-antibiotics. These drugs share similar privileged antimycobacterial drug scaffold.
MOLECULAR DIVERSITY
(2022)
Review
Pharmacology & Pharmacy
Zheng Zhao, Philip E. Bourne
Summary: Determining protein-ligand interaction characteristics and mechanisms is crucial to the drug discovery process. The systematic protein-ligand interaction fingerprint (IFP) approach has been successfully applied to investigate proteome-wide protein-ligand interactions for drug development. This strategy has been used to reveal polypharmacology, predict promising targets, uncover binding mechanisms, and demonstrate resistant mechanisms.
DRUG DISCOVERY TODAY
(2022)
Article
Biochemistry & Molecular Biology
Shimei Qin, Wan Li, Hongzheng Yu, Manyi Xu, Chao Li, Lei Fu, Shibin Sun, Yuehan He, Junjie Lv, Weiming He, Lina Chen
Summary: Drug repositioning is an effective approach to develop drugs for complex diseases like cancer and network-based computational biology approaches have been successfully applied to drug repurposing. In this study, a new strategy for network-based drug repositioning against cancer was developed. By constructing a cancer-related drug similarity network and quantifying the correlation score of each drug with specific cancer, potential repositionable drugs were identified and confirmed by clinical trial articles and databases. The targets of these drugs were significantly associated with the prognosis of NSCLC and provided valuable perspective for drug repurposing in cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Debby D. Wang, Moon-Tong Chan, Hong Yan
Summary: This study examines the importance and application of protein-ligand interaction fingerprints (IFPs) in protein binding affinity prediction, comparing different types of IFP models and highlighting the potential of atom-pair-counts-based and substructure-based IFPs in target-specific and generic scoring tasks.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Jingbo Yang, Denan Zhang, Lei Liu, Guoqi Li, Yiyang Cai, Yan Zhang, Hongbo Jin, Xiujie Chen
Summary: This article integrated the features of chemical-genomics and pharmaco-genomics to establish a drug-substructure-indication network for predicting therapeutic effects, demonstrating high accuracy and reliability.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Hailin Chen, Zuping Zhang, Jingpu Zhang
Summary: This research utilized integrated drug features to improve the accuracy of drug repositioning and proposed a fusion method. The results showed that the integration of similarity measurements had the best performance in predicting drug-disease associations.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Miriam R. Ferrandez, Savins Puertas-Martin, Juana L. Redondo, Horacio Perez-Sanchez, Pilar M. Ortigosa
Summary: Virtual screening methods are important for finding molecules with similar properties. The new tool, 2L-GO-Pharm, requires less computational effort than OptiPharm and improves solution quality by reducing evaluations needed. It enhances searchability with limitations and implements a balanced approach to exploration and exploitation of the search space.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Medicinal
Gen Li, Qing-Qing Dai, Guo-Bo Li
Summary: Metalloenzymes are enzymes that rely on metal ions, and comparing their active sites is crucial for enzyme design, function research, and inhibitor development. MeCOM is a method for comparing metalloenzyme active sites, which can accurately identify and compare active sites, evaluate similarity, and establish new associations between metalloenzymes.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemical Research Methods
Yiran Huang, Yongjin Bin, Pingfan Zeng, Wei Lan, Cheng Zhong
Summary: Drug repositioning is an important approach for predicting new disease indications for existing drugs. This paper proposes a neighborhood interaction-based method called NetPro for drug repositioning via label propagation. Experimental results show that NetPro can effectively identify potential drug-disease associations and achieve better prediction performance than existing methods. Case studies demonstrate that NetPro is capable of predicting promising candidate disease indications for drugs.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Saeid Maghsoudi, Bahareh Taghavi Shahraki, Fatemeh Rameh, Masoomeh Nazarabi, Yousef Fatahi, Omid Akhavan, Mohammad Rabiee, Ebrahim Mostafavi, Eder C. Lima, Mohammad Reza Saeb, Navid Rabiee
Summary: This review provides an overview of computational strategies and their applications in drug discovery, with a focus on chemogenomics and drug repositioning as emerging disciplines for coronavirus drug and target discovery. It showcases the special advantages of computer-aided drug discovery methods in rapidly finding drugs for deadly viruses like the coronavirus through molecular docking, chemogenomics, and drug repositioning.
CHEMICAL BIOLOGY & DRUG DESIGN
(2022)
Review
Biochemical Research Methods
Ashwin Dhakal, Cole McKay, John J. Tanner, Jianlin Cheng
Summary: New drug production can take over 12 years and cost around $2.6 billion, with the COVID-19 pandemic emphasizing the need for more powerful computational methods in drug discovery. This review focuses on computational approaches using artificial intelligence (AI) to predict protein-ligand interactions, particularly in deep learning methods. The correlation between protein-ligand interaction aspects and the proposal to study them together could lead to more accurate machine learning-based prediction strategies.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Pharmacology & Pharmacy
Abbas Kabir, Aaron Muth
Summary: Polypharmacology refers to the concept where a molecule can interact with two or more targets simultaneously, offering advantages over traditional single-targeting molecules. Multi-targeting drugs are more efficacious and effective in complex diseases like cancer. Predicting and intentionally incorporating promiscuity in molecules can lead to the design of polypharmacological drugs, which have numerous applications in drug repurposing. Despite being more difficult to design, with current technologies and information, it is plausible for researchers to unlock the advantages of polypharmacological drugs.
PHARMACOLOGICAL RESEARCH
(2022)
Article
Pharmacology & Pharmacy
C. Hutterer, S. Hamilton, M. Steingruber, I. Zeittraeger, H. Bahsi, N. Thuma, Z. Naing, Z. Oerfi, L. Oerfi, E. Socher, H. Sticht, W. Rawlinson, S. Chou, V. J. Haupt, M. Marschall
ANTIVIRAL RESEARCH
(2016)
Article
Pharmacology & Pharmacy
V. Joachim Haupt, Jesus E. Aguilar Uvalle, Sebastian Salentin, Simone Daminelli, Franziska Leonhardt, Janez Konc, Michael Schroeder
CURRENT PHARMACEUTICAL DESIGN
(2016)
Article
Chemistry, Medicinal
Tanja Stular, Samo Lesnik, Kaja Rozman, Julia Schink, Mitja Zdouc, An Ghysels, Feng Liu, Courtney C. Aldrich, V. Joachim Haupt, Sebastian Salentin, Simone Daminelli, Michael Schroeder, Thierry Langer, Stanislav Gobec, Dusanka Janezic, Janez Konc
JOURNAL OF MEDICINAL CHEMISTRY
(2016)
Article
Oncology
Joerg C. Heinrich, Sainitin Donakonda, V. Joachim Haupt, Petra Lennig, Yixin Zhang, Michael Schroeder
Article
Biochemical Research Methods
Christoph Baldow, Sebastian Salentin, Michael Schroeder, Ingo Roeder, Ingmar Glauche
PLOS COMPUTATIONAL BIOLOGY
(2017)
Article
Biochemical Research Methods
Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder, Dirk Labudde
PLOS COMPUTATIONAL BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Sebastian Salentin, Melissa F. Adasme, Joerg C. Heinrich, V. Joachim Haupt, Simone Daminelli, Yixin Zhang, Michael Schroeder
SCIENTIFIC REPORTS
(2017)
Article
Multidisciplinary Sciences
Melissa F. Adasme, Daniele Parisi, Kristien Van Belle, Sebastian Salentin, V. Joachim Haupt, Gary S. Jennings, Joerg-Christian Heinrich, Jean Herman, Ben Sprangers, Thierry Louat, Yves Moreau, Michael Schroeder
Article
Biochemistry & Molecular Biology
Alfredo Juarez-Saldivar, Michael Schroeder, Sebastian Salentin, V. Joachim Haupt, Emma Saavedra, Citlali Vazquez, Francisco Reyes-Espinosa, Veronica Herrera-Mayorga, Juan Carlos Villalobos-Rocha, Carlos A. Garcia-Perez, Nuria E. Campillo, Gildardo Rivera
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Multidisciplinary Sciences
Florian Kaiser, Sarah Krautwurst, Sebastian Salentin, V. Joachim Haupt, Christoph Leberecht, Sebastian Bittrich, Dirk Labudde, Michael Schroeder
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Melissa F. Adasme, Sarah Naomi Bolz, Lauren Adelmann, Sebastian Salentin, V. Joachim Haupt, Adriana Moreno-Rodriguez, Benjamin Nogueda-Torres, Veronica Castillo-Campos, Lilian Yepez-Mulia, Jose A. De Fuentes-Vicente, Gildardo Rivera, Michael Schroeder
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Sarah Naomi Bolz, Sebastian Salentin, Gary Jennings, V. Joachim Haupt, Jared Sterneckert, Michael Schroeder
Summary: Mutations in LRRK2 are a frequent cause of Parkinson's disease, and reducing its kinase activity is considered a promising therapeutic strategy. Drug repositioning, comparing protein-ligand interactions in a large-scale screening, yielded potential LRRK2 inhibitors such as Sunitinib and Crizotinib. The study highlights the potential of structure-based methods for drug discovery and development amidst recent advancements in cryo-electron microscopy and structure prediction.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Melissa F. Adasme, Katja L. Linnemann, Sarah Naomi Bolz, Florian Kaiser, Sebastian Salentin, V. Joachim Haupt, Michael Schroeder
Summary: With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules becomes increasingly important. PLIP, a tool for protein-ligand interaction profiling, has been successful in detecting and visualizing these interactions, with applications ranging from characterizing docking experiments to evaluating novel ligand-protein complexes. Additionally, PLIP has been extended to encompass interactions with DNA and RNA, demonstrating its utility in scenarios such as cancer drug targeting DNA and RNA-protein complexes associated with neurological diseases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Claudio Duran, Simone Daminelli, Josephine M. Thomas, V. Joachim Haupt, Michael Schroeder, Carlo Vittorio Cannistraci
BRIEFINGS IN BIOINFORMATICS
(2018)