AlphaFold: a revolutionary AI-based protein structure prediction system and its applications in drug discovery research

Cardiovascular Drug ReviewsVolume 12, Issue 1 p. 16-31 Free to Read Pharmacology of RWJ 29009, A New Potassium Channel Activator Bruce P. Damiano, Corresponding Author Bruce P. Damiano Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PAAddress correspondence and reprint requests to Dr. Damiano, at Drug Discovery Research, R. W. Johnson Pharmaceutical Research Institute, Spring House, PA 19477.Search for more papers by this authorJoseph J. Salata, Joseph J. Salata Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorLawrence B. Katz, Lawrence B. Katz Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorAlan Gill, Alan Gill Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorDavid Lee, David Lee Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorPauline J. Sanfilippo, Pauline J. Sanfilippo Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorJeffrey B. Press, Jeffrey B. Press Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorRobert Falotico, Robert Falotico Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this author Bruce P. Damiano, Corresponding Author Bruce P. Damiano Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PAAddress correspondence and reprint requests to Dr. Damiano, at Drug Discovery Research, R. W. Johnson Pharmaceutical Research Institute, Spring House, PA 19477.Search for more papers by this authorJoseph J. Salata, Joseph J. Salata Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorLawrence B. Katz, Lawrence B. Katz Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorAlan Gill, Alan Gill Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorDavid Lee, David Lee Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorPauline J. Sanfilippo, Pauline J. Sanfilippo Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorJeffrey B. Press, Jeffrey B. Press Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this authorRobert Falotico, Robert Falotico Drug Discovery Research, The R. W. Johnson Pharmaceutical Research Institute, Spring House, PASearch for more papers by this author First published: March 1994 https://doi.org/10.1111/j.1527-3466.1994.tb00281.xAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Volume12, Issue1March 1994Pages 16-31 RelatedInformation

Drug discovery and development together are the complete practice of identifying a new drug and passing it to market. It covers all areas of cancer biology, from cell signaling pathways to tumor hypoxia and from angiogenesis to cell death pathways. The Egyptian Association for Cancer Research (EACR) successfully organized its annual international conference under the theme of “Anti-Cancer Drug Discovery, 21-22 April 2019 at Tanta University convention Center, Egypt. ACDD-2019 was an excellent opportunity to gather national researchers and international researchers from the USA, China, Japan, KSA, and other countries to share their interest in drug discovery and development. The conference included 3 main sessions on day 1 and 8 sessions on day 2. Day 1 included 13 keynote speakers covering different subjects in anti-cancer drug discovery and based on nanoparticles, gene therapy, immunotherapy, and natural and synthetic compounds. Day 2 focused on the roles of the center of excellence of scientific research in drug discovery, parasite and marine compounds and cancer, natural and synthetic anti-cancer drugs, molecular oncology and cancer stem cells, and cancer immunology and immunotherapy. About 600 participants attended the conference including undergraduate and postgraduate students as well as faculty members from different colleges, universities, and research centers in Egypt. ACDD-2019 (http://acdd.tanta.edu.eg/) represented an outstanding opportunity for sharing thoughts and ideas for collaborative research in anti-cancer drug discovery and development from chemical synthesis to the clinic.

Description: New promising tools for drug development and discovery researchers This contributed work features state–of–the–science reviews of the structure, function, and modulation of neuronal voltage–gated ion channels, with an emphasis on their new and emerging applications to drug discovery and development. The reviews, written by leading experts in the field, are either comprehensive reviews of particular voltage–gated ion channel members or in–depth reviews of topics relevant to multiple voltage–gated ion channel subfamilies. Structure, Function, and Modulation of Neuronal Voltage–Gated Ion Channels is divided into three logical sections: Section One: Neuronal Voltage–Gated Ion Channel Functions Section Two: Modulatory Mechanisms and Influences on Neuronal Voltage–Gated Ion Channel Function Section Three: Drug Discovery Targets and Technology Among the key topics addressed are: Biochemical and molecular mechanisms and pathways in neuronal voltage–gated ion channel regulation Physiological bases of targeting ion channels in disease Advances in screening technologies, and methods for regulating neuronal voltage–gated ion channels Custom–developed technologies for ion channel drug discovery Utility of neuronal voltage–gated ion channel targets for the development of new medicines in traditional and emerging therapeutic areas Collectively, this book's reviews provide students and researchers with many new tools and approaches for their current ion channel and drug discovery research. Moreover, the book points the direction to promising areas of investigation worthy of further study.

The drug discovery and the drug development processes represent a continuum of recursive activities that range from initial drug target identification to final Food and Drug Administration approval and marketing of a new therapeutic. Drug discovery, as its name implies, is more exploratory and less focused in many cases, whereas drug development has a clinically defined endpoint and a specific disease goal. Academia has historically made major contributions to this process at the early discovery phases. However, current trends in the organization of the pharmaceutical industry suggest an expanded role for academia in the near future. Megamergers among major pharmaceutical corporations indicate their movement toward a focus on end-stage clinical trials, manufacturing, and marketing. There has been a parallel increase in outsourcing of intermediate steps to specialty small pharmaceutical, biotechnology, and contract service companies. The new paradigm suggests that academia will play an increasingly important role at the proof-of-principle stage of basic and clinical drug discovery research, in training the future skilled work force, and in close partnerships with small pharmaceutical and biotechnology companies. However, academic drug discovery research faces a set of barriers to progress, the relative importance of which varies with the home institution and the details of the research area. These barriers fall into four general categories: (1) the historical administrative structure and environment of academia; (2) the structure and emphasis of peer review panels that control research funding by government and private agencies; (3) the organization and operation of the academic infrastructure; and (4) the structure and availability of specialized resources and information management. Selected examples of barriers to drug discovery and drug development research and training in academia are presented, as are some specific recommendations designed to minimize or circumvent these barriers. In some cases, precedents established by other disease-focused areas may be relevant to Alzheimer disease and related disorders, but the overall impact of any changes requires adaptation at the top of the administrative structures in academia and funding agencies to support and encourage cooperative efforts among faculty investigators.

Drug Discovery 2012 and Beyond

Localization of Organelle Proteins by Isotope Tagging: Current status and potential applications in drug discovery research

The Japanese synchrotron radiation facilities, Photon Factory (PF) and SPring-8, are actively promoting structural life science and drug discovery research through the Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS), a project of the Japan Agency for Medical Research and Development (AMED). These facilities support Integrative Structural Biology research, focusing on protein crystallography, BioSAXS, and single particle analysis with cryo-electron microscopy. BioSAXS is a valuable technique for elucidating the structure and properties of biological macromolecules in solution. The SAXS beamlines at PF and SPring-8, notably BL-10C/BL-15A2 at PF and BL38B1 at SPring-8, are equipped with state-of-the-art instruments and comprehensive measurement and analysis environments. The SEC-SAXS measurement system was initially developed at PF and subsequently refined at BL38B1 (Fig. #1). The system at PF employs Prominence-i and Nexera-i (SHIMADZU) HPLC systems with a single pump route. Conversely, the BL38B1 system also utilizes the Prominence (SHIMADZU) system but features two pump pathways, enabling independent buffer replacement of columns in one pathway during SEC-SAXS measurement in the other. Additionally in these systems, a fiber spectrophotometer, QEpro/QE65pro (Ocean Photonics), has been installed to perform simultaneous UV-visible spectroscopy measurements with SAXS using the same sample cell. The continuously measured SAXS 2D image data are converted to 1D using the software SAngler [1], subtracted buffer profiles measured just before sample injection, normalized to an absolute scale (typically using the scattering intensity of water), and outputted. We have also developed MOLASS [2], a fully automated analysis software for SEC-SAXS data. MOLASS integrates basic SAXS theory with linear algebra techniques such as low-rank matrix factorization and singular value decomposition to combine continuous SAXS profiles and UV-visible absorption spectra for highly accurate analysis. We are also advancing the installation of various time-resolved solution scattering systems. At PF, two systems are in operation: a traditional stopped-flow system and a new system using a microfluidic device made of COP resin [3]. At SPring-8, the same microfluidic system as at PF is being introduced, alongside the development of new stop-flow and pump-probe systems at the undulator beamline, BL40XU. These systems are tailored based on the difference in the beam abilities such as beam sizes and photon fluxes between the two facilities. In this presentation, we will introduce the current status of the development of the BioSAXS measurement and analysis systems, which has been a collaborative effort between PF and SPring-8.

Flow cytometry is a mainstay technique in cell biology research, where it is used for phenotypic analysis of mixed cell populations. Quantitative approaches have unlocked a deeper value of flow cytometry in drug discovery research. As the number of drug modalities and druggable mechanisms increases, there is an increasing drive to identify meaningful biomarkers, evaluate the relationship between pharmacokinetics and pharmacodynamics (PK/PD), and translate these insights into the evaluation of patients enrolled in early clinical trials. In this review, we discuss emerging roles for flow cytometry in the translational setting that supports the transition and evaluation of novel compounds in the clinic.

Transfection of siRNA and plasmid nucleic molecules to animal, microbial and plant cell cultures is a critical process in various research areas, including drug discovery, functional genomics and basic life science research. Till recent times, transfection of these exogenous molecules have been global in nature i.e. targeting all the cells in a culture and lacking capability to spatially confine the transfection to small populations of cells within a single culture. However, in emerging areas like high-throughput screening of large molecule libraries, there is a critical need to transfect multiple different molecules to locally specified regions of a single cell culture and monitor phenotypical changes in these different cell populations. In this study, we present a cell-based biochip that utilizes a microelectrode array to generate localized current density fields that induce electroporation to a targeted group of cells for site-specific transfection of exogenous molecules. More specifically, we optimize the transfection efficiency and viabilities for spatially controlled transfection of Alexa-Fluor-488 conjugated siRNA molecules into NIH3T3 fibroblast cell cultures. Optimal electroporation parameters are established at current density values ranging between 0.05-0.07 microA microm(-2) for high transfection efficiencies (>60%) while maintaining viability (>80%) on individual microelectrodes. Additionally, exogenous plasmid molecules are electroporated for site-specific GFP expression and monitored over 48 h in-situ. The microelectrode array technology reported here can therefore be potentially used for targeting specific cells in a culture with spatial precision and transfecting siRNA and plasmids. The microfabrication approach lends itself to significant high-throughput applications in drug-discovery research.

Translational research facilitates the application of basic scientific discoveries in clinical and community settings to prevent and treat human diseases. The translation of knowledge and innovations from basic laboratory experiments to point-of-care patient applications; production of new drugs, devices, and healthcare products; and promising treatments for patients is referred to as benchside to bedside transition. Numerous opportunities encompass translational research. However, there are several obstacles involved in the process that make the translational journey quite challenging. The major challenges that hamper the growth of translational research include insufficient resources, inadequate funding and infrastructure, shortage of qualified researchers, and lack of sufficient experience in essential techniques. Translational drug discovery and development is an exceedingly difficult, expensive, time-consuming, and risky process. Despite thousands of pharmaceutical companies working to develop and get new drugs to market, and billions of dollars spent every year, only a few new molecular entities (NMEs) receive marketing approval from the FDA per year. Translational drug discovery demands both the need for cooperation between clinical and pharmacological research and the significance of the role of academia in target identification and drug discovery, design, and development. This chapter highlights an overview of translational research in a drug discovery and development perspective. We further discussed associated opportunities and challenges, as well as possible strategies that could be used to overcome the challenges. Certain strategies like prioritizing research area, clearer vision on the project, committed team of researchers, established infrastructure, sufficient funding, and meaningful collaborations could be highly beneficial in accelerating the hunt to discover new drugs and for the establishment of successful translational drug discovery process.

Insight into biological pathways, identification of new targets and appropriate biomarkers are the prerequisites for drug discovery & development. This PhD thesis addresses the role of fundamental research in drug discovery in age-related Alzheimer’s disease (AD), and a cancer-related target, the cell cycle. The large economic impact of AD, exponentially increasing in the ageing societies of industrialised countries strongly urges for discovery and development of drugs and therapy-related tools. As a consequence, the interest for retinoids based on their confirmed involvement in the regulation of disease-related genes in neurodegenerative ailments including AD has been revived, even though details of their molecular modes of action remain to be elucidated. The first project described in this PhD thesis focuses on the regulation of alpha-, beta-, and gamma-secretases mediated by all-trans-retinoic acid (ATRA), the main metabolite of retinoids. Our findings support the hypothesis that ATRA is capable of regulating secretases in the anti-amyloidogenic sense at the levels of transcription, translation, and activation. Apart from increased alpha-secretase activity, we show a complex chain of regulatory events, resulting in impaired beta-secretase trafficking and its membranal localisation due to protein kinase C (PKC) activation by ATRA, resulting in enhanced secretion of soluble APPalpha. ATRA also affected activity, transcription and localisation of Presenilin 1, the functional core of the gamma-secretase, but had no effect on Presenilin 2. The experiments were performed in three neuronal and non-neuronal cell lines of human and murine origin, which allowed us to determine general mechanisms and cell line-specific differences in the ATRA-mediated regulation of secretases. Although control of gene expression by retinoids occurs mainly via genomic regulation of target genes, anti-amyloidogenic effects of retinoids have been attributed to their PKC-stimulating ability and subsequent activation of alpha-secretases only. Therefore, contribution of genomic and non-genomic control mechanisms to the regulation of BACE1, the main beta-secretase, by ATRA was examined in the second project. Our findings corroborated the role of PKC stimulation in the down-regulation of BACE1 at the transcriptional and translational levels, resulting in decrease of Abeta42 in the human embryonic kidney HEK 293 cell line. ATRA induced DNA-binding activity of its receptors RARbeta-RXR, and showed PKC- dependent activation of the transcription factors NFkB and AP-1, as revealed by electrophoretic mobility shift assay (EMSA). We show disruption of a PKC-modulated decrease of BACE1 mRNA and Abeta levels, when NFkB or AP-1 activity was blocked by BAY11-7082, NFkB inhibitor, or by the transfection of inhibitory DNA-oligonucleotides. For the first time PKC-signalling induced by retinoids could be linked to the transcriptional control of BACE1 regulation. The last project described in this PhD studied the role of ADAM17 in the the cell cycle. ADAM17 is gaining attention in the field of clinical research as a potential outcome biomarker in breast cancer and adenocarcinoma. However, a possible implication of ADAM17 in the cell cycle has not been investigated, since its role in cancer is usually considered in the context of epidermal growth factor receptor signalling. First, through a combination of mass spectrometry and biochemical methods, we identified alpha- and beta-tubulins as binding partners of ADAM17. This interaction was confirmed bidirectionally in the murine neuroblastoma N2a cell line, and the ADAM17 fragments involved in tubulin-binding were identified. Additionally, we showed co-localisation of ADAM17 and tubulins in the spindle of mitotic cells. Furthermore, we were able to show a cell cycle-dependent regulation of ADAM17 by over-expression of either full length or mature ADAM17 versions in N2a cell line and observed significantly increased invasiveness due to over-expression of mature ADAM17 form. Still, biological significance of the interaction between ADAM17 and tubulins remains to be discovered. Altogether, these studies examined existing theories, raised new hypothesis, and contributed to the identification of new targets and a clearer understanding of fundamental mechanisms.

The 4th International symposium entitled ‘‘Current Trends in Drug Discovery Research’’ (CTDDR-2010) was organized in the sprit of the 1st, 2nd, and 3rd CTDDR (2001, 2004, and 2007) symposia from February 17 to 21st, 2010. The symposium had a focus on the innovative drug discovery approaches for infectious and tropical diseases (malaria, filaria, leishmania, HIV, and tuberculosis), aging, genetic, metabolic and endocrine disorders (neurodegenerative, diabetes, obesity, CNSand CVSrelated disorders), and reproductive disorders (osteoporosis). The deliberations contained the cocktail of computational endeavors, innovative drug discovery approaches and indepth analysis of structure-activity relationships (SAR), new drug targets and state of art techniques for the syntheses of organic molecules of biological interest. A preliminary classification of sub-areas for discussions included cellular and molecular signaling, virtual library design and screening, system biology, drugs from nature/bioimaging and bioprospecting, molecular approaches to disease therapy, validated therapeutic targets, drug design, synthesis, QSAR, CADD, and CAMM, novel approaches to drug discovery, pharmacokinetics/pharmaceutical sciences, translational research, informatics in drug discovery, and preclinical/clinical trials. The symposium was an outstanding success as it covered the above topics in 56 lectures delivered in 16 sessions, 280 posters presented in 4 poster sessions. It provided a platform to about 600 researchers including 45 from other countries including USA, Germany, France, UK, Switzerland, Greece, Hungary, Denmark, Canada, South Africa, Russia, Italy, Belgium, Netherlands, Hong Kong, Japan, Egypt, Turkey, Australia and other countries for lively interactions during the 5-day deliberations. In this special issue, a total 68 manuscripts were submitted for publication. The manuscripts were peerreviewed by at least two experts in the field and 43 manuscripts were successful in navigating the process and were included in this particular issue of Medicinal Chemistry Research. I, as guest editor gratefully acknowledge the reviewers of manuscripts, Mr. A.S. Kushwaha for secretarial assistance, Dr. Stephen J. Cutler, his team and Birkhauser Verlag for providing all out support for successfully bringing out this special issue.

Translational research in drug discovery - current issues and perspectives.

Protein disordered regions are segments of a protein chain that do not adopt a stable structure. Thus far, a variety of protein disorder prediction methods have been developed and have been widely used, not only in traditional bioinformatics domains, including protein structure prediction, protein structure determination and function annotation, but also in many other biomedical fields. The relationship between intrinsically-disordered proteins and some human diseases has played a significant role in disorder prediction in disease identification and epidemiological investigations. Disordered proteins can also serve as potential targets for drug discovery with an emphasis on the disordered-to-ordered transition in the disordered binding regions, and this has led to substantial research in drug discovery or design based on protein disordered region prediction. Furthermore, protein disorder prediction has also been applied to healthcare by predicting the disease risk of mutations in patients and studying the mechanistic basis of diseases. As the applications of disorder prediction increase, so too does the need to make quick and accurate predictions. To fill this need, we also present a new approach to predict protein residue disorder using wide sequence windows that is applicable on the genomic scale.

Primary human hepatocytes are widely used to study drug metabolism and enzyme induction. However, primary hepatocytes rapidly lose their hepatic function in conventional 2D cultures. Recently, a microphysiological system that overcomes this drawback has been actively investigated and applied in drug discovery research. Such novel in vitro models are desirable for the evaluation of the metabolic clearance of drugs with low turnover, drug-induced liver injury, and chronic liver diseases like liver fibrosis. This article reviews the characteristics and recent advances in 3D-bioprinted human liver tissue models in drug discovery research.