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Otvos L, Wade JD. Big peptide drugs in a small molecule world. Front Chem 2023; 11:1302169. [PMID: 38144886 PMCID: PMC10740154 DOI: 10.3389/fchem.2023.1302169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023] Open
Abstract
A quarter of a century ago, designer peptide drugs finally broke through the glass ceiling. Despite the resistance by big pharma, biotechnology companies managed to develop injectable peptide-based drugs, first against orphan or other small volume diseases, and later for conditions affecting large patient populations such as type 2 diabetes. Even their lack of gastrointestinal absorption could be utilized to enable successful oral dosing against chronic constipation. The preference of peptide therapeutics over small molecule competitors against identical medical conditions can be achieved by careful target selection, intrachain and terminal amino acid modifications, appropriate conjugation to stability enhancers and chemical space expansion, innovative delivery and administration techniques and patient-focused marketing strategies. Unfortunately, however, pharmacoeconomical considerations, including the strength of big pharma to develop competing small molecule drugs, have somewhat limited the success of otherwise smart peptide-based therapeutics. Yet, with increasing improvement in peptide drug modification and formulation, these are continuing to gain significant, and growing, acceptance as desirable alternatives to small molecule compounds.
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Affiliation(s)
- Laszlo Otvos
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
- OLPE Pharmaceutical Consultants, Audubon, PA, United States
| | - John D. Wade
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
- School of Chemistry, University of Melbourne, Parkville, VIC, Australia
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Macalino SJY, Basith S, Clavio NAB, Chang H, Kang S, Choi S. Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. Molecules 2018; 23:E1963. [PMID: 30082644 PMCID: PMC6222862 DOI: 10.3390/molecules23081963] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022] Open
Abstract
The advent of advanced molecular modeling software, big data analytics, and high-speed processing units has led to the exponential evolution of modern drug discovery and better insights into complex biological processes and disease networks. This has progressively steered current research interests to understanding protein-protein interaction (PPI) systems that are related to a number of relevant diseases, such as cancer, neurological illnesses, metabolic disorders, etc. However, targeting PPIs are challenging due to their "undruggable" binding interfaces. In this review, we focus on the current obstacles that impede PPI drug discovery, and how recent discoveries and advances in in silico approaches can alleviate these barriers to expedite the search for potential leads, as shown in several exemplary studies. We will also discuss about currently available information on PPI compounds and systems, along with their usefulness in molecular modeling. Finally, we conclude by presenting the limits of in silico application in drug discovery and offer a perspective in the field of computer-aided PPI drug discovery.
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Affiliation(s)
- Stephani Joy Y Macalino
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Shaherin Basith
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Nina Abigail B Clavio
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Hyerim Chang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Soosung Kang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
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Young RJ, Leeson PD. Mapping the Efficiency and Physicochemical Trajectories of Successful Optimizations. J Med Chem 2018; 61:6421-6467. [DOI: 10.1021/acs.jmedchem.8b00180] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Robert J. Young
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul D. Leeson
- Paul Leeson Consulting Ltd., The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K
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Szekely G, Amores de Sousa MC, Gil M, Castelo Ferreira F, Heggie W. Genotoxic Impurities in Pharmaceutical Manufacturing: Sources, Regulations, and Mitigation. Chem Rev 2015; 115:8182-229. [DOI: 10.1021/cr300095f] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Gyorgy Szekely
- School of Chemical Engineering & Analytical Science, The University of Manchester, The Mill, Sackville Street, Manchester M13 9PL, United Kingdom
| | - Miriam C. Amores de Sousa
- Department
of Bioengineering and Institute for Bioengineering and Biosciences
(iBB), Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Marco Gil
- Hovione FarmaCiencia SA, R&D, Sete Casas, 2674-506, Loures, Portugal
| | - Frederico Castelo Ferreira
- Department
of Bioengineering and Institute for Bioengineering and Biosciences
(iBB), Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal
| | - William Heggie
- Hovione FarmaCiencia SA, R&D, Sete Casas, 2674-506, Loures, Portugal
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Tschammer N, Kokornaczyk AK, Strunz AK, Wünsch B. Selective and Dual Targeting of CCR2 and CCR5 Receptors: A Current Overview. CHEMOKINES 2014; 14. [PMCID: PMC7123309 DOI: 10.1007/7355_2014_40] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The chemokine receptor 2 (CCR2) and chemokine receptor 5 (CCR5) are important mediators of leukocyte trafficking in inflammatory processes. The emerging evidence for a role of CCR2 and CCR5 receptors in human inflammatory diseases led to a growing interest in CCR2- and CCR5-selective antagonists. In this review, we focus on the recent development of selective CCR2/CCR5 receptor ligands and dual antagonists. Several compounds targeting CCR2, e.g., INCB8761 and MK0812, were developed as promising candidates for clinical trials, but failed to show clinical efficacy as presumed from preclinical models. The role of CCR5 receptors as the second co-receptor for the HIV-host cell fusion led to the development of various CCR5-selective ligands. Maraviroc is the first CCR5-targeting drug for the treatment of HIV-1 infections on the market. The role of CCR5 receptors in the progression of inflammatory processes fueled the use of CCR5 antagonists for the treatment of rheumatoid arthritis. Unfortunately, the use of maraviroc for the treatment of rheumatoid arthritis failed due to its inefficacy. Some of the ligands, e.g., TAK-779 and TAK-652, were also found to be dual antagonists of CCR2 and CCR5 receptors. The fact that CCR2 and CCR5 receptor antagonists contribute to the treatment of inflammatory diseases renders the development of dual antagonists as promising novel therapeutic strategy.
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Affiliation(s)
- Nuska Tschammer
- Dept. of Chemistry and Pharmacy, Friedrich Alexander University, Erlangen, Germany
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Junker A, Schepmann D, Yamaguchi J, Itami K, Faust A, Kopka K, Wagner S, Wünsch B. Diverse modifications of the 4-methylphenyl moiety of TAK-779 by late-stage Suzuki–Miyaura cross-coupling. Org Biomol Chem 2014; 12:177-86. [DOI: 10.1039/c3ob41873a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.
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Affiliation(s)
- Gregory Sliwoski
- Jr., Center for Structural Biology, 465 21st Ave South, BIOSCI/MRBIII, Room 5144A, Nashville, TN 37232-8725.
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Affiliation(s)
- James Pease
- Leukocyte Biology Section, National Heart and Lung Institute, Faculty of Medicine, MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, Imperial College London, London SW7 2AZ, U.K
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Synthesis and biological evaluation of novel piperidin-4-ol derivatives. MONATSHEFTE FUR CHEMIE 2012. [DOI: 10.1007/s00706-011-0645-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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An in situ oxidation strategy towards overcoming hERG affinity. Bioorg Med Chem Lett 2010; 20:6400-4. [PMID: 20934332 DOI: 10.1016/j.bmcl.2010.09.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 09/14/2010] [Accepted: 09/15/2010] [Indexed: 11/20/2022]
Abstract
In an effort to overcome hERG affinity with a lead compound, several S-oxide and N-oxide analogues were synthesised with a much improved hERG profile but low in vivo absorption. This led to the implementation of an in situ oxidation strategy wherein a sulfide was dosed orally and systemic levels of the corresponding sulfoxide and sulfone were monitored. SAR and pharmacokinetic data to support this as a possible strategy are presented, although ultimately the approach was shown not to be suitable due to very low levels of active circulating metabolites.
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Qian K, Morris-Natschke SL, Lee KH. HIV entry inhibitors and their potential in HIV therapy. Med Res Rev 2009; 29:369-93. [PMID: 18720513 DOI: 10.1002/med.20138] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This review discusses recent progress in the development of anti-HIV agents targeting the viral entry process. The three main classes (attachment inhibitors, co-receptor binding inhibitors, and fusion inhibitors) are further broken down by specific mechanism of action and structure. Many of these inhibitors are in advanced clinical trials, including the HIV maturation inhibitor bevirimat, from the authors' laboratories. In addition, the CCR5 inhibitor maraviroc has recently been FDA-approved. Possible roles for these agents in anti-HIV therapy, including treatment of virus resistant to current drugs, are also discussed.
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Affiliation(s)
- Keduo Qian
- Natural Products Research Laboratories, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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Barber CG, Blakemore DC, Chiva JY, Eastwood RL, Middleton DS, Paradowski KA. 1-Amido-1-phenyl-3-piperidinylbutanes - CCR5 antagonists for the treatment of HIV. Part 1. Bioorg Med Chem Lett 2009; 19:1075-9. [PMID: 19171484 DOI: 10.1016/j.bmcl.2009.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 01/05/2009] [Accepted: 01/06/2009] [Indexed: 10/21/2022]
Abstract
The development of a new class of CCR5 antagonist replacing the tropane core of maraviroc by piperidine with a branched N-substituent is described. Compound 15h shows good whole cell antiviral activity together with microsomal stability and only weak activity at the hERG ion channel.
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Affiliation(s)
- Christopher G Barber
- Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent CT13 9NJ, UK.
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Jones BC, Middleton DS, Youdim K. 6 Cytochrome P450 Metabolism and Inhibition: Analysis for Drug Discovery. PROGRESS IN MEDICINAL CHEMISTRY 2009; 47:239-63. [DOI: 10.1016/s0079-6468(08)00206-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Mastrolorenzo A, Maresca A, Rusconi S, Supuran CT. Update on the development of HIV entry inhibitors. ACTA ACUST UNITED AC 2008. [DOI: 10.2217/17469600.2.5.479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
HIV fusion and entry are two steps in the viral lifecycle that can be targeted by several classes of antiviral drugs. The discovery of chemokines focused the attention on cellular co-receptors used by the virus for entering cells, and on the various steps of such processes that are subject to interactions with small molecules. Intense research has led to a wide range of effective compounds that are able to inhibit these initial steps of viral replication. All steps in the process of HIV entry into the cell may be targeted by specific compounds, grouped into three main classes (attachment inhibitors, co-receptor binding inhibitors and fusion inhibitors), which may be developed as novel antiretrovirals. Thus, several inhibitors of the gp120–CD4 interaction have been discovered (e.g., zintevir and BMS-378806). Small molecule chemokine receptor antagonists acting as HIV entry inhibitors have also been described recently, including those which interact with both the CXCR4 co-receptor (e.g., AMD3100, AMD3465, ALX40-4C, T22, T134 and T140) and CCR5 co-receptor antagonists (TAK-779, TAK-220, E913, AK-602 and NSC 651016 in clinical trials). Recently, a third family of antivirals started to be used clinically (in addition to reverse transcriptase and protease inhibitors), with the advent of enfuvirtide (T20), the first fusion inhibitor to be approved as an anti-HIV agent. Some of these compounds demonstrated in vitro synergism with other classes of antivirals, thus offering the rationale for their combination in therapies for HIV-infected individuals. Many HIV entry and fusion inhibitors are currently being investigated in controlled clinical trials, and a number of them are bioavailable as oral formulations. In 2007, the US FDA approved maraviroc as an anti-HIV agent. Maraviroc is the product of a medicinal chemistry effort initiated following identification of an imidazopyridine CCR5 ligand from a high-throughput screen of the Pfizer compound file. Maraviroc demonstrated potent antiviral activity against all CCR5-tropic HIV-1 viruses tested, including 43 primary isolates from various clades and diverse geographic origin. Maraviroc was active against 200 clinically derived HIV-1 envelope-recombinant pseudoviruses, 100 of which were derived from viruses resistant to existing drug classes. Furthermore, in October 2007, the FDA announced the approval of raltegravir for the treatment of HIV-1 infection as part of combination antiretroviral therapy in treatment-experienced patients with evidence of HIV-1 replication despite optimized background antiretroviral therapy. At present, raltegravir is the only drug in the integrase inhibitor class approved for clinical use. With the approval of raltegravir, oral agents targeting all three constitutive viral enzymes, reverse transcriptase, protease and integrase, are now represented in FDA-approved therapies.
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Affiliation(s)
- Antonio Mastrolorenzo
- Università degli Studi di Firenze, Dipartimento di Scienze Dermatologiche, Centro MTS, Via degli Alfani 37, I-50121 Florence, Italy
| | - Alfonso Maresca
- Università degli Studi di Firenze, Dipartimento di Chimica, Laboratorio di Chimica Bioinorganica, Via della Lastruccia, 3, Rm. 188, I-50019 Sesto Fiorentino (Florence), Italy
| | - Stefano Rusconi
- Dipartimento di Scienze Cliniche “Luigi Sacco”, Cattedra di Malattie Infettive e Tropicali, Università degli Studi, Ospedale Luigi Sacco, Via GB Grassi 74, 20157 Milano, Italy
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Dipartimento di Chimica, Laboratorio di Chimica Bioinorganica, Via della Lastruccia, 3, Rm. 188, I-50019 Sesto Fiorentino (Florence), Italy
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Chapter 19 Small Molecule CCR5 and CXCR4-Based Viral Entry Inhibitors for Anti-HIV Therapy Currently in Development. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2007. [DOI: 10.1016/s0065-7743(07)42019-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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