Drug Development
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On the Organization of a Drug Discovery Platform
DOI: 10.5772/intechopen.73170 ProvisionalChapter chapter 2 On the Organization of a Drug Discovery Platform Jean A. Boutin,A. Boutin, Olivier NosjeanOlivier Nosjean and Gilles FerryGilles Ferry Additional information is available at the end of the chapter http://dx.doi.org/10.5772/intechopen.73170 Abstract Some of the most exciting parts of work in the pharmaceutical industry are the steps lead- ing up to drug discovery. This process can be oversimplified by describing it as a screen- ing campaign involving the systematic testing of many compounds in a test relevant to a given pathology. This naïve description takes place without taking into consideration the numerous key steps that led up to the screening or the steps that might follow. The present chapter describes this whole process as it was conducted in our company dur- ing our early drug discovery activities. First, the purpose of the procedures is described and rationalized. Next follows a series of mostly published examples from our own work illustrating the various steps of the process from cloning to biophysics, including expression systems and membrane-bound protein purifications. We believe that what is described here presents an example of how pharmaceutical industry research can orga- nize its platform(s) when the goal is to find and qualify a new preclinical drug candidate using cutting-edge technologies and a lot of hard work. Keywords: drug discovery, validation, cloning & expression, biophysics, structural biology, organization 1. Introduction Drug discovery involves a suite of processes as part of a program aimed at finding drug thera- pies for diseases. These programs encompass many different scientific steps from validation of the target (or attempts to do so) and characterization of the hits until the selection of can- didates for medicinal chemistry programs. -
Predicting Strategies for Lead Optimization Via Learning to Rank
IPSJ Transactions on Bioinformatics Vol.11 41–47 (Dec. 2018) [DOI: 10.2197/ipsjtbio.11.41] Original Paper Predicting Strategies for Lead Optimization via Learning to Rank Nobuaki Yasuo1,2,a) Keisuke Watanabe1 Hideto Hara3 Kentaro Rikimaru3 Masakazu Sekijima1,4,b) Received: August 21, 2018, Accepted: September 18, 2018 Abstract: Lead optimization is an essential step in drug discovery in which the chemical structures of compounds are modified to improve characteristics such as binding affinity, target selectivity, physicochemical properties, and tox- icity. We present a concept for a computational compound optimization system that outputs optimized compounds from hit compounds by using previous lead optimization data from a pharmaceutical company. In this study, to predict the drug-likeness of compounds in the evaluation function of this system, we evaluated and compared the ability to correctly predict lead optimization strategies through learning to rank methods. Keywords: lead optimization, learning to rank, computer-aided drug design, machine learning computer-aided drug discovery (CADD), which has been utilized 1. Introduction since the 1960s, are also leading current drug discovery. The During drug discovery, enormous attempts are being made to methods of CADD can be combined with various biological data identify better drug candidates. Since the cost of drug discovery including genomic sequence, protein tertiary structure, and chem- has been drastically increased, recently the process of drug dis- ical structure, and can be utilized in various steps in drug discov- covery typically takes 12–14 years [1] and costs approximately ery: target identification, compound screening, and ADME (ab- 2.6 billion USD [2]. The process of drug discovery is sometimes sorption, distribution, metabolism, excretion, toxicity) properties likened to looking for a needle in a haystack; it is the process prediction [9], [10], [11]. -
Functional Selectivity and Classical Concepts of Quantitative Pharmacology
JPET Fast Forward. Published on June 27, 2006 as DOI: 10.1124/jpet.106.104463 JPET ThisFast article Forward. has not been Published copyedited andon formatted.June 27, The 2006 final versionas DOI:10.1124/jpet.106.104463 may differ from this version. JPET #104463 PiP Title Page Functional selectivity and classical concepts of quantitative pharmacology Jonathan D. Urban, William P. Clarke, Mark von Zastrow, David E. Nichols, Brian Kobilka, Harel Weinstein, Jonathan A. Javitch, Bryan L. Roth, Arthur Christopoulos Patrick M. Sexton, Keith J. Miller, Michael Spedding, Richard B. Mailman Downloaded from Curriculum in Toxicology (JDU, RBM) and Departments of Pharmacology, Psychiatry Medicinal Chemistry (BLR, RBM), and Neurology (RBM), University of North Carolina, Chapel Hill, NC Department of Pharmacology, University of Texas Health Science Center, San Antonio, jpet.aspetjournals.org TX (WPC) Departments of Psychiatry and Cellular and Molecular Pharmacology, University of California, San Francisco, CA (MvZ) at ASPET Journals on September 25, 2021 Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, IN (DEN) Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA Department of Physiology and Biophysics, and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY (HW) Center for Molecular Recognition, and Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, New York, NY (JJ) Department of Pharmacology, Monash University, Clayton, Victoria, Australia (AC, PMS) Obesity Department, Pharmaceutical Research Institute, Bristol-Myers Squibb, Princeton, NJ (KJM) Institute de Recherches Servier, Suresnes 92150, France MS) 1 Copyright 2006 by the American Society for Pharmacology and Experimental Therapeutics. -
Clinical Pharmacology 1: Phase 1 Studies and Early Drug Development
Clinical Pharmacology 1: Phase 1 Studies and Early Drug Development Gerlie Gieser, Ph.D. Office of Clinical Pharmacology, Div. IV Objectives • Outline the Phase 1 studies conducted to characterize the Clinical Pharmacology of a drug; describe important design elements of and the information gained from these studies. • List the Clinical Pharmacology characteristics of an Ideal Drug • Describe how the Clinical Pharmacology information from Phase 1 can help design Phase 2/3 trials • Discuss the timing of Clinical Pharmacology studies during drug development, and provide examples of how the information generated could impact the overall clinical development plan and product labeling. Phase 1 of Drug Development CLINICAL DEVELOPMENT RESEARCH PRE POST AND CLINICAL APPROVAL 1 DISCOVERY DEVELOPMENT 2 3 PHASE e e e s s s a a a h h h P P P Clinical Pharmacology Studies Initial IND (first in human) NDA/BLA SUBMISSION Phase 1 – studies designed mainly to investigate the safety/tolerability (if possible, identify MTD), pharmacokinetics and pharmacodynamics of an investigational drug in humans Clinical Pharmacology • Study of the Pharmacokinetics (PK) and Pharmacodynamics (PD) of the drug in humans – PK: what the body does to the drug (Absorption, Distribution, Metabolism, Excretion) – PD: what the drug does to the body • PK and PD profiles of the drug are influenced by physicochemical properties of the drug, product/formulation, administration route, patient’s intrinsic and extrinsic factors (e.g., organ dysfunction, diseases, concomitant medications, -
Drugs and Drug Development: Making a Drug
Drugs and drug development: Making a drug Developing a novel drug Drug development is a long and expensive process A drug can be developed in a whole host of different ways. Constant improvement in technology has transformed drug design over the past few decades. Now, many laboratories in both universities and pharmaceutical companies make use of computers, robotics and artificial intelligence to aid in drug design. These techniques coupled with more traditional methods are becoming increasingly successful in designing novel drugs. One commonality between all the methods of drug design is that they are fraught with challenges. A pharmaceutical company may start with thousands of chemical compounds as potential drug candidates. Rigorous testing will whittle this down to a single chemical compound that can then be licensed to treat patients. Developing drugs is a risky and expensive business, but the potential profits are huge. The following step-by-step process provides a guide to how a compound in the laboratory becomes a disease-fighting drug. Option 1 explains the process of transforming initial research in a university lab (or biotechnology company) into a potential drug – about a quarter of drugs approved by the FDA between 1998 and 2007 began in this way. The remaining three-quarters began in pharmaceutical companies, as explained in option 2. STEP 1 – OPTION 1: Origins in the research lab In universities and research institutes all over the globe, many scientists dedicate their lives to understanding the molecular details of disease – how disease works. By using animal models, usually mice, they are able to identify specific biochemical pathways that are altered by the disease. -
Medicinal Chemistry for Drug Discovery | Charles River
Summary Medicinal chemistry is an integral part of bringing a drug through development. Our medicinal chemistry approach enables clients to benefit from efficient navigation of the early drug discovery process through to delivery of preclinical candidates. DISCOVERY Click to learn more Medicinal Chemistry for Drug Discovery Medicinal Chemistry A Proven Track Record in Drug Discovery Services: Our medicinal chemistry team has experience in progressing small molecule drug discovery programs across a broad range • Target identification of therapeutic areas and gene families. Our scientists are skilled in the design and synthesis of novel pharmacologically active - Capture Compound® mass compounds and understand the challenges facing modern drug discovery. Together, they are cited as inventors on over spectrometry (CCMS) 350 patents and have identified 80 preclinical candidates for client organizations across a variety of therapeutic areas. As • Hit-finding strategies project leaders, our chemists are fundamental in driving the program strategy and have consistently empowered our clients’ - Optimizing high-throughput success. A high proportion of candidates regularly progress to the clinic, and our first co-invented drug, Belinostat, received screening (HTS) hits marketing approval in 2015. As an organization, Charles River has worked on 85% of the therapies approved in 2018. • Hit-to-lead We have a deep understanding of the factors that drive medicinal chemistry design: structure-activity relationship (SAR), • Lead optimization biology, physical chemistry, drug metabolism and pharmacokinetics (DMPK), pharmacokinetic/pharmacodynamic (PK/PD) • Patent strategy modelling, and in vivo efficacy. Charles River scientists are skilled in structure-based and ligand-based design approaches • Preparation for IND filing utilizing our in-house computer-aided drug design (CADD) expertise. -
Early-Phase Drug Discovery
Early-Phase Drug Discovery In partnership with the North Carolina Translational & Clinical Sciences (NC TraCs) Institute, RTI International is participating in the Early-Phase Drug Discovery Service (EPDD) to help researchers navigate challenges in the drug discovery process and move technologies toward development. This new RTI-based NC TraCS service can provide researchers with biological assay development and optimization, hit or lead identification, medicinal chemistry optimization, in vitro absorption, distribution, metabolism, excretion, and toxicology (ADMET), and in vivo pharmacokinetics. Overview Early stages of the drug discovery process contain hurdles that must be cleared before more robust drug development can commence. Once a molecular target is selected, drug discovery begins with identification of a hit and progresses toward a lead candidate through a series of structural optimizations. If no hit or lead molecules exist, a researcher must have a validated biological assay that can be optimized for high-throughput screening (HTS). Screening hits typically do not possess optimal drug- like properties. Therefore, their affinity, selectivity, and pharmacokinetic (PK) properties must be improved through structural modifications by a medicinal chemist. Once acceptable drug-like properties have been achieved, efficacy is validated through proof-of-principle studies in vivo. The most promising set of optimized compounds is then slated for further development. The EPDD can assist researchers by providing target development and assay miniaturization, identification of hits through HTS in a 25,000-compound library, lead optimization, in vitro ADMET assays, and preliminary in vivo PK studies. Services will be provided on a tiered basis. Tier 1 consists of consulting services designed to inform the researcher of gaps in his or her early-phase drug discovery plan. -
Pharmacogenetic Testing: a Tool for Personalized Drug Therapy Optimization
pharmaceutics Review Pharmacogenetic Testing: A Tool for Personalized Drug Therapy Optimization Kristina A. Malsagova 1,* , Tatyana V. Butkova 1 , Arthur T. Kopylov 1 , Alexander A. Izotov 1, Natalia V. Potoldykova 2, Dmitry V. Enikeev 2, Vagarshak Grigoryan 2, Alexander Tarasov 3, Alexander A. Stepanov 1 and Anna L. Kaysheva 1 1 Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; [email protected] (T.V.B.); [email protected] (A.T.K.); [email protected] (A.A.I.); [email protected] (A.A.S.); [email protected] (A.L.K.) 2 Institute of Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; [email protected] (N.V.P.); [email protected] (D.V.E.); [email protected] (V.G.) 3 Institute of Linguistics and Intercultural Communication, Sechenov University, 119992 Moscow, Russia; [email protected] * Correspondence: [email protected]; Tel.: +7-499-764-9878 Received: 2 November 2020; Accepted: 17 December 2020; Published: 19 December 2020 Abstract: Pharmacogenomics is a study of how the genome background is associated with drug resistance and how therapy strategy can be modified for a certain person to achieve benefit. The pharmacogenomics (PGx) testing becomes of great opportunity for physicians to make the proper decision regarding each non-trivial patient that does not respond to therapy. Although pharmacogenomics has become of growing interest to the healthcare market during the past five to ten years the exact mechanisms linking the genetic polymorphisms and observable responses to drug therapy are not always clear. Therefore, the success of PGx testing depends on the physician’s ability to understand the obtained results in a standardized way for each particular patient. -
Reigniting Pharmaceutical Innovation Through Holistic Drug Targeting
Drug Discovery Reigniting pharmaceutical innovation through holistic drug targeting Modern drug discovery approaches take too long, are too expensive, have too many clinical failures and uncertain outcomes. There are many reasons for this unsustainable business model, but primarily, the approaches are not comprehensively holistic. Secondly, none of the pharmaceutical companies openly share the reasons for the failure of their clinical candidates in real time to effectively navigate the ‘industry’ from committing the same mistakes. It is time for the pharmaceutical industry to embrace, metaphorically speaking, a community-driven ‘Wikipedia’ or ‘Waze’-type shared-knowledge, openly- accessible innovation model to harvest data and create a crowd-sourced path towards a safer and faster road to the discovery and development of life-saving medicines. This may be a bitter pill for Pharma to swallow, but one that ought to be given serious consideration. The time is now for a paradigm shift towards multi-target-network polypharmacology drugs exalting symphonic or concert performance with occasional soloists to reignite pharmaceutical innovation. rom the turn of the 20th century, pharma- and ultra-high throughput workflows enabled By Dr Anuradha Roy, cognosy and ethnopharmacology combined screening of millions of compounds to identify hit Professor Bhushan F with anecdotal clinical evidence accumulat- can didates for lead development. Despite billions Patwardhan and ed over centuries of hands-on knowledge from pri- of dollars spent on R&D, only a fraction of the Dr Rathnam mordial disease management practices, albeit with molecules identified from the screening operations Chaguturu uncertain outcomes, formed the basis for the devel- find their way into clinical trials. -
Comparative Thermodynamics of Partial Agonist Binding to An
COMPARATIVE THERMODYNAMICS OF PARTIAL AGONIST BINDING TO AN AMPA RECEPTOR BINDING DOMAIN A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Madeline Martínez May 2015 © 2015 Madeline Martínez ALL RIGHTS RESERVED Comparative Thermodynamics of Partial Agonist Binding to an AMPA Receptor Binding Domain Madeline Martínez, Ph.D. Cornell University 2015 AMPA receptors, ligand-gated cation channels endogenously activated by glutamate, mediate the majority of rapid excitatory synaptic transmission in the vertebrate central nervous system and are crucial for information processing within neural networks. Their involvement in a variety of neuropathologies and injured states makes them important therapeutic targets, and understanding the forces that drive the interactions between the ligands and protein binding sites is a key element in the development and optimization of potential drug candidates. Calorimetric studies yield quantitative data on the thermodynamic forces that drive binding reactions. This information can help elucidate mechanisms of binding and characterize ligand- induced conformational changes, as well as reduce the potential unwanted effects in drug candidates. The studies presented here characterize the thermodynamics of binding of a series of 5’substituted willardiine analogues, partial agonists to the GluA2 LBD under several conditions. The moiety substitutions (F, Cl, I, H, and NO2) explore a range of electronegativity, pKa, radii, and h-bonding capability. Competitive binding of these ligands to glutamate-bound GluA2 LBD at different pH conditions demonstrates the effects of charge in the enthalpic and entropic components of the Gibb’s free energy of binding. -
Development of a FLIPR Assay for the Simultaneous Identification of Mrgd
Hindawi Publishing Corporation Journal of Biomedicine and Biotechnology Volume 2010, Article ID 326020, 8 pages doi:10.1155/2010/326020 Research Article Development of a FLIPR Assay for the Simultaneous Identification of MrgD Agonists and Antagonists from a Single Screen Seena K. Ajit,1, 2 Mark H. Pausch,2 Jeffrey D. Kennedy,2 and Edward J. Kaftan2 1 Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 North 15th Street, MS number 488, Philadelphia, PA 19102, USA 2 Neuroscience Discovery, Pfizer Global Research and Development, CN 8000, Princeton, NJ 08543, USA Correspondence should be addressed to Seena K. Ajit, [email protected] Received 1 April 2010; Revised 8 July 2010; Accepted 6 August 2010 Academic Editor: John V. Moran Copyright © 2010 Seena K. Ajit et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MrgD, a member of the Mas-related gene family, is expressed exclusively in small diameter IB4+ neurons in the dorsal root ganglion. This unique expression pattern, the presence of a single copy of MrgD in rodents and humans, and the identification of a putative ligand, beta-alanine, make it an experimentally attractive therapeutic target for pain with limited likelihood of side effects. We have devised a high throughput calcium mobilization assay that enables identification of both agonists and antagonists from a single screen for MrgD. Screening of the Library of Pharmacologically Active Compounds (LOPAC) validated this assay approach, and we identified both agonists and antagonists active at micromolar concentrations in MrgD expressing but not in parental CHO-DUKX cell line. -
DMPK) Studies Are Critical to Efficient Drug Discovery Programs and Successful Delivery of Candidate Molecules
Summary Discovery drug metabolism and pharmacokinetics (DMPK) studies are critical to efficient drug discovery programs and successful delivery of candidate molecules. DISCOVERY Drug Metabolism and Pharmacokinetics (DMPK) Click to learn more Supporting Discovery Research DMPK Services The identification and inclusion of appropriate DMPK studies is key to the success of discovery research by helping to de-risk • In vitro ADME candidate molecules and improve project productivity through more targeted chemical synthesis and progression of the right compounds. Charles River’s flexible and collaborativeDMPK team offers a variety of partnerships and pricing structures to suit • Physicochemical properties client needs. In addition to fee-for-service assays and expertise, we can embed our DMPK scientists within existing integrated • Metabolic stability chemistry programs as core team members of multidisciplinary project teams. We offer a wealth of experience in a range of • Drug-drug interactions therapeutic areas and biological targets and can help support strategy and implementation of appropriate screening cascades. • Distribution • Safety • High-throughput and automation Chemistry • Pharmacokinetics (PK) support • Bioanalysis and Biology pharmacokinetic support DMPK Questions for our chemists? Visit https://www.criver.com/ consult-pi-ds-questions-for-our- chemists EVERY STEP OF THE WAY www.criver.com In Vitro ADME As compound potency improves during hit-to-lead and lead optimization, in vitro ADME assays provide necessary data to establish insight into the key physiochemical properties and structural motifs that will provide the targeted candidate profile. Our in vitro ADME scientists have established a suite of assays that routinely support drug discovery programs, continue to work on the development and validation of new assays, and regularly monitor assay performance.