Advanced machine-learning techniques in drug discovery.

Abstract:

:The popularity of machine learning (ML) across drug discovery continues to grow, yielding impressive results. As their use increases, so do their limitations become apparent. Such limitations include their need for big data, sparsity in data, and their lack of interpretability. It has also become apparent that the techniques are not truly autonomous, requiring retraining even post deployment. In this review, we detail the use of advanced techniques to circumvent these challenges, with examples drawn from drug discovery and allied disciplines. In addition, we present emerging techniques and their potential role in drug discovery. The techniques presented herein are anticipated to expand the applicability of ML in drug discovery.

journal_name

Drug Discov Today

journal_title

Drug discovery today

authors

Elbadawi M,Gaisford S,Basit AW

doi

10.1016/j.drudis.2020.12.003

subject

Has Abstract

pub_date

2020-12-05 00:00:00

eissn

1359-6446

issn

1878-5832

pii

S1359-6446(20)30521-3

pub_type

杂志文章,评审
  • Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation.

    abstract::In recent years there has been a dramatic increase in the number of freely accessible online databases serving the chemistry community. The internet provides chemistry data that can be used for data-mining, for computer models, and integration into systems to aid drug discovery. There is however a responsibility to en...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2012.02.013

    authors: Williams AJ,Ekins S,Tkachenko V

    更新日期:2012-07-01 00:00:00

  • Value your compound management team!

    abstract::The Discussion Forum provides a medium for airing your views on any issues related to the pharmaceutical industry and obtaining feedback and discussion on these views from others in the field. You can discuss issues that get you hot under the collar, practical problems at the bench, recently published literature, or j...

    journal_title:Drug discovery today

    pub_type: 杂志文章

    doi:10.1016/s1359-6446(01)01816-5

    authors: Ray BJ

    更新日期:2001-06-01 00:00:00

  • Understanding the checkpoint blockade in lung cancer immunotherapy.

    abstract::Immunotherapies have changed the treatment strategy of some types of tumor including melanoma and, more recently, non-small-cell lung cancer (NSCLC). Immune checkpoints are crucial for the maintenance of self-tolerance and it is known that some tumors use checkpoint systems to evade antitumor immune response. The trea...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2017.05.016

    authors: Dal Bello MG,Alama A,Coco S,Vanni I,Grossi F

    更新日期:2017-08-01 00:00:00

  • Optimizing the use of open-source software applications in drug discovery.

    abstract::Drug discovery is a time consuming and costly process. Recently, a trend towards the use of in silico computational chemistry and molecular modeling for computer-aided drug design has gained significant momentum. This review investigates the application of free and/or open-source software in the drug discovery process...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/S1359-6446(05)03692-5

    authors: Geldenhuys WJ,Gaasch KE,Watson M,Allen DD,Van der Schyf CJ

    更新日期:2006-02-01 00:00:00

  • DNA-nanorobot-guided thrombin-inducing tumor infarction: raising new potential clinical concerns.

    abstract::DNA-nanorobot-guided thrombin-inducing tumor infarction (DNA NanorobotTh-ITI) is emerging as a powerful therapeutic strategy for treatment of solid cancers. The technology represents a major advance in the application of DNA nanotechnology for anticancer therapy. More importantly, the technology is being translated fr...

    journal_title:Drug discovery today

    pub_type: 杂志文章

    doi:10.1016/j.drudis.2020.03.005

    authors: Zheng K,Kros JM,Li J,Zheng PP

    更新日期:2020-06-01 00:00:00

  • Methods to identify and optimize small molecules interacting with RNA (SMIRNAs).

    abstract::RNAs, particularly noncoding RNAs (ncRNAs), are becoming increasingly important therapeutic targets, because they are causative and antagonists of human disease. Indeed, aberrant RNA structural elements and expression deregulate biological processes. In this review, we describe methodologies to discover and optimize s...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2019.06.019

    authors: Ursu A,Vézina-Dawod S,Disney MD

    更新日期:2019-10-01 00:00:00

  • Targeting mutant huntingtin for the development of disease-modifying therapy.

    abstract::Huntington's disease (HD) is a progressive and fatal neurodegenerative disease, and the most common inherited CAG repeat disorder. A polyglutamine expansion in the N-terminus of the huntingtin protein (HTT) leads to protein misfolding and downstream pathogenic processes culminating in widespread functional impairment ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2012.06.017

    authors: Appl T,Kaltenbach L,Lo DC,Terstappen GC

    更新日期:2012-11-01 00:00:00

  • Controlling 2-arachidonoylglycerol metabolism as an anti-inflammatory strategy.

    abstract::The endocannabinoid system is implicated in, and regulates, several physiological processes, ranging from food intake and energy balance to pain and inflammation. 2-Arachidonoylglycerol (2-AG) is a full agonist at the cannabinoid receptors which classically mediate its effects. The activity of this bioactive lipid is ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2013.07.009

    authors: Alhouayek M,Masquelier J,Muccioli GG

    更新日期:2014-03-01 00:00:00

  • 3D in vitro models of tumors expressing EGFR family receptors: a potent tool for studying receptor biology and targeted drug development.

    abstract::Carcinomas overexpressing EGFR family receptors are of high clinical importance, because the receptors have prognostic value and are used as molecular targets for anticancer therapy. Insufficient drug efficacy necessitates further in-depth research of the receptor biology and improvement in preclinical stages of drug ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2018.09.003

    authors: Sokolova EA,Vodeneev VA,Deyev SM,Balalaeva IV

    更新日期:2019-01-01 00:00:00

  • Targeted delivery for regenerative medicines: an untapped opportunity for drug conjugates.

    abstract::Regenerative approaches are promising avenues to effectively cure diseases rather than merely treating symptoms, but are associated with concerns around proliferation in other organs. Given that targeted delivery holds the promise of delivering a drug precisely to its desired site of action, usually with the prospect ...

    journal_title:Drug discovery today

    pub_type: 杂志文章

    doi:10.1016/j.drudis.2016.12.004

    authors: Valeur E,Knerr L,Ölwegård-Halvarsson M,Lemurell M

    更新日期:2017-06-01 00:00:00

  • The MEK5/ERK5 signalling pathway in cancer: a promising novel therapeutic target.

    abstract::Conventional mitogen-activated protein kinase (MAPK) family members are among the most sought-after oncogenic effectors for the development of novel human cancer treatment strategies. MEK5/ERK5 has been the less-studied MAPK subfamily, despite its increasingly demonstrated relevance in the growth, survival, and differ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2016.06.010

    authors: Simões AE,Rodrigues CM,Borralho PM

    更新日期:2016-10-01 00:00:00

  • Development of HIV-1 integrase inhibitors: recent molecular modeling perspectives.

    abstract::Of the three viral enzymes essential to HIV replication, HIV-1 integrase (IN) is gaining popularity as a target for the antiviral therapy of AIDS. Substantial work focusing on IN has been done over the past three decades, which has facilitated and led to the approval of three drugs. Here, we discuss in detail the deve...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2015.07.012

    authors: Su M,Tan J,Lin CY

    更新日期:2015-11-01 00:00:00

  • Psoriasis: pathological mechanisms, current pharmacological therapies, and emerging drug delivery systems.

    abstract::Psoriasis is a chronic autoimmune skin disorder triggered by either genetic factors, environmental factors, life style, or a combination thereof. Clinical investigations have identified pathogenesis, such as T cell and cytokine-mediated, genetic disposition, antimicrobial peptides, lipocalin-2, galectin-3, vaspin, fra...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2020.09.023

    authors: Rapalli VK,Waghule T,Gorantla S,Dubey SK,Saha RN,Singhvi G

    更新日期:2020-12-01 00:00:00

  • EU marketing authorization review of orphan and non-orphan drugs does not differ.

    abstract::Marketing authorization application dossiers of 17 orphan drugs (ODs) and 51 non-ODs evaluated by the European Medicines Agency (EMA) in the period 2009-2010 were compared. We aimed to identify whether any differences existed between ODs and non-ODs in number and type of deficits brought forward during the EMA review,...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2013.06.012

    authors: Putzeist M,Mantel-Teeuwisse AK,Llinares J,Gispen-De Wied CC,Hoes AW,Leufkens HG

    更新日期:2013-10-01 00:00:00

  • Respiratory syncytial virus: recent progress towards the discovery of effective prophylactic and therapeutic agents.

    abstract::Although respiratory syncytial virus (RSV) was discovered in 1955, the burden associated with this infectious agent on all population groups is only now beginning to be fully appreciated. The successful launch of the humanized monoclonal antibody Synagis (developed by MedImmune, Gaithersburg, MD, USA), as a prophylact...

    journal_title:Drug discovery today

    pub_type: 杂志文章

    doi:10.1016/s1359-6446(00)01500-2

    authors: Meanwell NA,Krystal M

    更新日期:2000-06-01 00:00:00

  • Expanded Access Programs, compassionate drug use, and Emergency Use Authorizations during the COVID-19 pandemic.

    abstract::The US Food and Drug Administration (FDA) Expanded Access (EA) Program, which allows for compassionate uses of unapproved therapeutics and diagnostics outside of clinical trials, has gained significant traction during the Coronavirus 2019 (COVID-19) pandemic. While development of vaccines has been the major focus, unc...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2020.11.025

    authors: Rizk JG,Forthal DN,Kalantar-Zadeh K,Mehra MR,Lavie CJ,Rizk Y,Pfeiffer JP,Lewin JC

    更新日期:2020-11-27 00:00:00

  • Model-based drug discovery: implementation and impact.

    abstract::Model-based drug discovery (MBDDx) aims to build and continuously improve the quantitative understanding of the relation between drug exposure (target engagement) efficacy and safety, to support target validation; to define compound property criteria for lead optimization and safety margins; to set the starting dose; ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2013.05.012

    authors: Visser SA,Aurell M,Jones RD,Schuck VJ,Egnell AC,Peters SA,Brynne L,Yates JW,Jansson-Löfmark R,Tan B,Cooke M,Barry ST,Hughes A,Bredberg U

    更新日期:2013-08-01 00:00:00

  • Atomic force microscopy and drug discovery.

    abstract::Atomic force microscopy is being used ever more widely in biological imaging, because of its unique ability to provide structural information at the single molecule level and under near-physiological conditions. Detailed topographic images of potential drug targets, such as proteins and DNA, have been produced, and th...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/S1359-6446(03)02905-2

    authors: Edwardson JM,Henderson RM

    更新日期:2004-01-15 00:00:00

  • Gastric bypass surgery mimetic approaches.

    abstract::Gastric bypass surgery is effectively a polypharmacological approach for treatment of obesity, type 2 diabetes and nonalcoholic steatohepatitis (NASH). The gastric bypass mimetic approaches reviewed are fixed-dose combinatorial pharmacological approaches. There are two key concepts incorporated into these gastric bypa...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2017.04.009

    authors: Boettcher BR

    更新日期:2017-08-01 00:00:00

  • Phage display-derived peptides as therapeutic alternatives to antibodies.

    abstract::Peptide-based drugs are now viable alternatives to biopharmaceuticals, such as antibodies. Most of the past limitations of peptides have been removed by new technologies, so that peptides now face similar hurdles to antibodies. Phage-display technology provides novel peptides that bind protein targets with high affini...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/S1359-6446(04)03104-6

    authors: Ladner RC,Sato AK,Gorzelany J,de Souza M

    更新日期:2004-06-15 00:00:00

  • Improvement of preclinical animal models for autoimmune-mediated disorders via reverse translation of failed therapies.

    abstract::The poor translational validity of autoimmune-mediated inflammatory disease (AIMID) models in inbred and specific pathogen-free (SPF) rodents underlies the high attrition of new treatments for the corresponding human disease. Experimental autoimmune encephalomyelitis (EAE) is a frequently used preclinical AIMID model....

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2014.03.023

    authors: 't Hart BA,Jagessar SA,Kap YS,Haanstra KG,Philippens IH,Serguera C,Langermans J,Vierboom M

    更新日期:2014-09-01 00:00:00

  • Immunotherapies in cutaneous pathologies: an overview.

    abstract::Skin is a vital protective organ, the main role of which is to provide a physical barrier and to prevent the entry of pathogens. Various pathologies, such as atopic dermatitis (AD), psoriasis (PSO), or skin cancers, can affect the skin, and all show a high and increasing prevalence. Many antibodies are currently used ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2020.10.023

    authors: Baylet A,Laclaverie M,Marchand L,Bordes S,Closs-Gonthier B,Delpy L

    更新日期:2021-01-01 00:00:00

  • Meeting the discovery challenge of drug-resistant infections: progress and focusing resources.

    abstract::Following multiple warnings from governments and health organisations, there has been renewed investment, led by the public sector, in the discovery of novel antimicrobials to meet the challenge of rising levels of drug-resistant infection, particularly in the case of resistance to antibiotics. Initiatives have also b...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2018.11.015

    authors: Dougan G,Dowson C,Overington J,Next Generation Antibiotic Discovery Symposium Participants.

    更新日期:2019-02-01 00:00:00

  • Intravitreal nanoparticles for retinal delivery.

    abstract::Intravitreal injection is one of the major administration routes for the treatment of posterior ocular diseases. Intravitreal therapeutics usually suffer from unsatisfactory efficacy owing to fast clearance from the vitreous humour and insufficient distribution into the retina. Engineered nanoparticles have been appli...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2019.05.005

    authors: Huang X,Chau Y

    更新日期:2019-08-01 00:00:00

  • Cancer therapy via modulation of micro RNA levels: a promising future.

    abstract::Micro RNAs (miRNAs) are a class of naturally occurring ∼ 22 nt long non-coding small RNA molecules that regulate the expression of a wide range of genes involved in development, growth, proliferation and apoptosis. miRNAs are evolutionarily conserved from plants to animals, and they regulate and fine-tune a diverse ar...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2010.07.003

    authors: Kota SK,Balasubramanian S

    更新日期:2010-09-01 00:00:00

  • In vitro bioassays to evaluate beneficial and adverse health effects of botanicals: promises and pitfalls.

    abstract::This review provides an update on the promises and pitfalls when using in vitro bioassays to evaluate beneficial and adverse health effects of botanicals and botanical preparations. Important issues addressed in the paper are: (i) the type of assays and biological effects available; (ii) false-positives, false-negativ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2017.05.002

    authors: Prinsloo G,Papadi G,Hiben MG,de Haan L,Louisse J,Beekmann K,Vervoort J,Rietjens IMCM

    更新日期:2017-08-01 00:00:00

  • Molecular epigenetic targets for liver diseases: current challenges and future prospects.

    abstract::Advanced chemotherapy fails to treat liver cancer but recent progress in understanding epigenetic modifications have witnessed promising clinical outcomes. Epigenetic alteration is the alteration of epigenomes (surrounding histone proteins) without changing the DNA sequence. Such epigenetic mechanisms include histone ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2017.07.008

    authors: Zeidler R,de Freitas Soares BL,Bader A,Giri S

    更新日期:2017-11-01 00:00:00

  • The targeted delivery of cancer drugs across the blood-brain barrier: chemical modifications of drugs or drug-nanoparticles?

    abstract::One of the most challenging problems, if not the most challenging, in drug development is not to develop drugs to treat diseases of the central nervous system (CNS), but to manage to distribute them to the CNS across the blood-brain barrier (BBB) using transvascular routes following intravenous administration. The dev...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2008.09.005

    authors: Juillerat-Jeanneret L

    更新日期:2008-12-01 00:00:00

  • Recent computational advances in the identification of allosteric sites in proteins.

    abstract::Allosteric modulators have the potential to fine-tune protein functional activity. Therefore, the targeting of allosteric sites, as a strategy in drug design, is gaining increasing attention. Currently, it is not trivial to find and characterize new allosteric sites by experimental approaches. Alternatively, computati...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2014.07.012

    authors: Lu S,Huang W,Zhang J

    更新日期:2014-10-01 00:00:00

  • Homologous recombination in human iPS and ES cells for use in gene correction therapy.

    abstract::The emergence of induced pluripotent stem (iPS) cell technology has shifted gene correction therapy toward reality. Crucial issues are ensuring the safety of using iPS cell technology in patients and discovering how best to transfer genetically manipulated iPS cells back into patients. One key issue that has hindered ...

    journal_title:Drug discovery today

    pub_type: 杂志文章,评审

    doi:10.1016/j.drudis.2010.01.006

    authors: Nakayama M

    更新日期:2010-03-01 00:00:00