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Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 57313

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Prof. Dr. Libor Grubhoffer

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Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic
Interests: arthropod-borne viruses as causative agent of severe diseases of human and animals, especially flavivirues transmitted by ticks; interaction of tick-borne flaviviruses with host cells, innate immunity against flaviviruses; structural and non-structural proteins of flaviviruses, especially Tick-borne Encephalitis virus; ticks as vectors of flaviviruses and borrelia spirochetes; vaccines agains ticks and tick transmitted pathogens

Prof. Dr. Masanori Baba

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Research and International Affairs 1-21-24, Korimoto, Kagoshima 890-8580, Japan
Interests: studying the pathogenesis and therapy of retrovirus (HIV-1 and HTLV-1) infections; identification and development of antiviral drugs against severe fever with thrombocytopenia syndrome virus (SFTSV) and anti-adult T-cell leukemia (ATL) drugs; investigations on anti-HBV agents

Special Issue Information

Dear Colleagues,

This Special Issue of Molecules is dedicated to Prof. Dr. Erik De Clercq on the occasion of his 80th anniversary. Professors Libor Grubhoffer and Masanori Baba, along with the Editors of Molecules, invite scientists to join us in celebrating Prof. Dr. Erik De Clercq’s exceptional achievements by contributing original research articles as well as reviews.

Prof. Dr. Erik De Clercq was born on 28 March 1941 in Dendermonde (Belgium) and later graduated as Medical Doctor (MD) in 1966 and Philosophical Doctor (PhD) in 1972. He has been Full Professor at the Faculty of Medicine (KU Leuven) since his appointment in 1977. He spent two years at Stanford University (1968–1970), and the rest of his career at the Rega Institute for Medical Research (KU Leuven). Prof. De Clercq holds an Honorary Doctorate from the Universities of Ghent, Athens, Ferrara, Shandong, Prague (Charles), Česke Budějovice, Tours, and Hull and is an honorary citizen of the town of Hamme (Belgium). He was named inventor of the year in 2008 (EU), and Laureate of the Dr. Paul Janssen Prize in 2010. He is best known for his co-invention (together with Dr. Antonín Holý) of the anti-HIV drug, tenofovir. Prof. De Clercq has taught courses in Microbiology (Virology) and Biochemistry at KU Leuven and KU Leuven Campus Kortrijk. Since 2006, he has been serving as Emeritus Professor at the KU Leuven, but has continued teaching, since 2007 until today, the course on “Biochemistry at the Service of Medicine” to Bachelor and Master students from the Universities of Česke Budějovice (Budweis) and Linz.

Highlights in the scientific career of (Prof. Dr.) Erik De Clercq:

In 1968, discovery of several inducers of interferon (e.g., polyacrylic acid).
In 1975, inhibition of the murine reverse transcriptase by suramin, the first compound ever to be demonstrated as an inhibitor of HIV infection both in vitro (citation of text from Mitsuya et al. on E. De Clercq’s article in Cancer Letters) and in vivo (humans).
In 1979, discovery of BVDU as a potent and selective anti-HSV-1 agent, later marketed over the entire world for the treatment of VZV infections (herpes zoster), following original report of E. De Clercq et al.
In 1978, discovery of DHPA, together with acyclovir, the first acyclic nucleoside found to exhibit antiviral activity.
In 1980, the cloning and expression of human β-interferon and elucidation of its primary structure.
In 1982, identification of the amino acid esters of acyclovir from which the valine ester (valacyclovir) would become its successor on the worldwide market.
In 1986, discovery of acyclic nucleoside phosphonates (i.e., HPMPA, PMEA) as a new class of broad-spectrum anti-DNA virus agents.
In 1987, discovery of d4T (2’,3’-dideoxy-2’,3’-didehydro thymidine), later marketed as stavudine, for the treatment of HIV infections.
In 1989 and 1990, discovery of NNRTIs (non-nucleoside reverse transcriptase inhibitors) with not only one but two prototypes, the HEPT and TIBO derivatives. The latter would eventually lead to the development of rilpivirine for the drug market.
In 1993, discovery of PMPA, which later became known as tenofovir, would become the most popular anti-HIV drug worldwide for the treatment of HIV infections.
In 1998, tenofovir was derivatized to its prodrug, tenofovir disoproxil fumarate (TDF); in 2005 a new prodrug of tenofovir, tenofovir alafenamide (TAF) was developed, and TDF and TAF have been marketed worldwide for the treatment of HIV and hepatitis B virus (HBV) infections.
Tenofovir (as TDF or TAF), in combination with emtricitabine, has become the only compound in the world to be used in the prophylaxis (prevention) of HIV infections (commonly referred to as PrEP: pre-exposure prophylaxis).
As of 2020, 15 marketed drugs containing tenofovir (TDF or TAF) have become available all over the world.
In 2000, a new nucleoside analogue, Cf-1743, was discovered, that is even more potent than BVDU, and yields great potential as a valine ester (fermavir, FV-100) for the treatment of VZV infections.
Since 2018, a new phosphonate analogue (derivatized from PMEG), has become available for the treatment of (malignant) lymphomas in dogs (Tanovea®).
Originally described as an anti-HIV agent in 1992 (paper sponsored by the Nobel Prize winner Mx Perutz) and 1994, a bicyclam derivative, AMD-3100 (plerixafor), has been found to be effective as a stem cell mobilizer (Mozobil®), and has been licensed for autologous transplantation in patients with multiple myeloma or non-Hodgkin’s lymphoma.

Prof. Dr. Libor Grubhoffer
Prof. Dr. Masanori Baba
Guest Editors

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Published Papers (11 papers)

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Research

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21 pages, 5305 KiB

Open AccessArticle

From Repurposing to Redesign: Optimization of Boceprevir to Highly Potent Inhibitors of the SARS-CoV-2 Main Protease

by Matthias Göhl, Linlin Zhang, Haifa El Kilani, Xinyuanyuan Sun, Kaixuan Zhang, Mark Brönstrup and Rolf Hilgenfeld

Molecules 2022, 27(13), 4292; https://doi.org/10.3390/molecules27134292 - 4 Jul 2022

Cited by 15 | Viewed by 3027

Abstract

The main protease (M^pro) of the betacoronavirus SARS-CoV-2 is an attractive target for the development of treatments for COVID-19. Structure-based design is a successful approach to discovering new inhibitors of the M^pro. Starting from crystal structures of the M^pro in complexes with the Hepatitis C virus NS3/4A protease inhibitors boceprevir and telaprevir, we optimized the potency of the alpha-ketoamide boceprevir against the M^pro by replacing its P1 cyclobutyl moiety by a γ-lactam as a glutamine surrogate. The resulting compound, MG-78, exhibited an IC₅₀ of 13 nM versus the recombinant M^pro, and similar potency was observed for its P1′ N-methyl derivative MG-131. Crystal structures confirmed the validity of our design concept. In addition to SARS-CoV-2 M^pro inhibition, we also explored the activity of MG-78 against the M^pro of the alphacoronavirus HCoV NL63 and against enterovirus 3C proteases. The activities were good (0.33 µM, HCoV-NL63 M^pro), moderate (1.45 µM, Coxsackievirus 3C^pro), and relatively poor (6.7 µM, enterovirus A71 3C^pro), respectively. The structural basis for the differences in activities was revealed by X-ray crystallo-graphy. We conclude that the modified boceprevir scaffold is suitable for obtaining high-potency inhibitors of the coronavirus M^pros but further optimization would be needed to target enterovirus 3C^pros efficiently. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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26 pages, 1214 KiB

Open AccessArticle

Synthesis, Structure–Activity Relationships, and Antiviral Profiling of 1-Heteroaryl-2-Alkoxyphenyl Analogs as Inhibitors of SARS-CoV-2 Replication

by Dorothée Bardiot, Laura Vangeel, Mohamed Koukni, Philippe Arzel, Marleen Zwaagstra, Heyrhyoung Lyoo, Patrick Wanningen, Shamshad Ahmad, Linlin Zhang, Xinyuanyuan Sun, Adrien Delpal, Cecilia Eydoux, Jean-Claude Guillemot, Eveline Lescrinier, Hugo Klaassen, Pieter Leyssen, Dirk Jochmans, Karolien Castermans, Rolf Hilgenfeld, Colin Robinson, Etienne Decroly, Bruno Canard, Eric J. Snijder, Martijn J. van Hemert, Frank van Kuppeveld, Patrick Chaltin, Johan Neyts, Steven De Jonghe and Arnaud Marchand Show full author list Hide full author list

Molecules 2022, 27(3), 1052; https://doi.org/10.3390/molecules27031052 - 4 Feb 2022

Cited by 4 | Viewed by 3914

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has led to a pandemic, that continues to be a huge public health burden. Despite the availability of vaccines, there is still a need for small-molecule antiviral drugs. In an effort to identify novel and drug-like hit matter that can be used for subsequent hit-to-lead optimization campaigns, we conducted a high-throughput screening of a 160 K compound library against SARS-CoV-2, yielding a 1-heteroaryl-2-alkoxyphenyl analog as a promising hit. Antiviral profiling revealed this compound was active against various beta-coronaviruses and preliminary mode-of-action experiments demonstrated that it interfered with viral entry. A systematic structure–activity relationship (SAR) study demonstrated that a 3- or 4-pyridyl moiety on the oxadiazole moiety is optimal, whereas the oxadiazole can be replaced by various other heteroaromatic cycles. In addition, the alkoxy group tolerates some structural diversity. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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19 pages, 847 KiB

Open AccessEditor’s ChoiceArticle

Synthesis and Anti-HIV Activity of a Novel Series of Isoquinoline-Based CXCR4 Antagonists

by Mastaneh Safarnejad Shad, Sandra Claes, Eline Goffin, Tom Van Loy, Dominique Schols, Steven De Jonghe and Wim Dehaen

Molecules 2021, 26(20), 6297; https://doi.org/10.3390/molecules26206297 - 18 Oct 2021

Cited by 3 | Viewed by 2801

Abstract

An expansion of the structure–activity relationship study of CXCR4 antagonists led to the synthesis of a series of isoquinolines, bearing a tetrahydroquinoline or a 3-methylpyridinyl moiety as head group. All compounds were investigated for CXCR4 affinity and antagonism in competition binding and calcium mobilization assays, respectively. In addition, the anti-HIV activity of all analogues was determined. All compounds showed excellent activity, with compound 24c being the most promising one, since it displayed consistently low nanomolar activity in the various assays. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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16 pages, 3138 KiB

Open AccessArticle

Searching Anti-Zika Virus Activity in 1H-1,2,3-Triazole Based Compounds

by Willyenne M. Dantas, Valentina N. M. de Oliveira, Diogo A. L. Santos, Gustavo Seabra, Prem P. Sharma, Brijesh Rathi, Lindomar J. Pena and Ronaldo N. de Oliveira

Molecules 2021, 26(19), 5869; https://doi.org/10.3390/molecules26195869 - 28 Sep 2021

Cited by 9 | Viewed by 2695

Abstract

Zika virus (ZIKV) is a mosquito-borne virus belonging to the Flaviviridae family and is responsible for an exanthematous disease and severe neurological manifestations, such as microcephaly and Guillain-Barré syndrome. ZIKV has a single strand positive-sense RNA genome that is translated into structural and non-structural (NS) proteins. Although it has become endemic in most parts of the tropical world, Zika still does not have a specific treatment. Thus, in this work we evaluate the cytotoxicity and antiviral activities of 14 hybrid compounds formed by 1H-1,2,3-triazole, naphthoquinone and phthalimide groups. Most compounds showed low cytotoxicity to epithelial cells, specially the 3b compound. After screening with all compounds, 4b was the most active against ZIKV in the post-infection test, obtaining a 50% inhibition concentration (IC₅₀) of 146.0 µM and SI of 2.3. There were no significant results for the pre-treatment test. According to the molecular docking compound, 4b was suggested with significant binding affinity for the NS5 RdRp protein target, which was further corroborated by molecular dynamic simulation studies. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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13 pages, 3484 KiB

Open AccessArticle

Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase

by Jiří Gregor, Kateřina Radilová, Jiří Brynda, Jindřich Fanfrlík, Jan Konvalinka and Milan Kožíšek

Molecules 2021, 26(4), 1007; https://doi.org/10.3390/molecules26041007 - 14 Feb 2021

Cited by 8 | Viewed by 4742

Abstract

Influenza A virus (IAV) encodes a polymerase composed of three subunits: PA, with endonuclease activity, PB1 with polymerase activity and PB2 with host RNA five-prime cap binding site. Their cooperation and stepwise activation include a process called cap-snatching, which is a crucial step in the IAV life cycle. Reproduction of IAV can be blocked by disrupting the interaction between the PB2 domain and the five-prime cap. An inhibitor of this interaction called pimodivir (VX-787) recently entered the third phase of clinical trial; however, several mutations in PB2 that cause resistance to pimodivir were observed. First major mutation, F404Y, causing resistance was identified during preclinical testing, next the mutation M431I was identified in patients during the second phase of clinical trials. The mutation H357N was identified during testing of IAV strains at Centers for Disease Control and Prevention. We set out to provide a structural and thermodynamic analysis of the interactions between cap-binding domain of PB2 wild-type and PB2 variants bearing these mutations and pimodivir. Here we present four crystal structures of PB2-WT, PB2-F404Y, PB2-M431I and PB2-H357N in complex with pimodivir. We have thermodynamically analysed all PB2 variants and proposed the effect of these mutations on thermodynamic parameters of these interactions and pimodivir resistance development. These data will contribute to understanding the effect of these missense mutations to the resistance development and help to design next generation inhibitors. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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Review

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12 pages, 2585 KiB

Open AccessReview

Newly Emerging Strategies in Antiviral Drug Discovery: Dedicated to Prof. Dr. Erik De Clercq on Occasion of His 80th Anniversary

by Shujing Xu, Dang Ding, Xujie Zhang, Lin Sun, Dongwei Kang, Boshi Huang, Xinyong Liu and Peng Zhan

Molecules 2022, 27(3), 850; https://doi.org/10.3390/molecules27030850 - 27 Jan 2022

Cited by 16 | Viewed by 5075

Abstract

Viral infections pose a persistent threat to human health. The relentless epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global health problem, with millions of infections and fatalities so far. Traditional approaches such as random screening and optimization of lead compounds by organic synthesis have become extremely resource- and time-consuming. Various modern innovative methods or integrated paradigms are now being applied to drug discovery for significant resistance in order to simplify the drug process. This review provides an overview of newly emerging antiviral strategies, including proteolysis targeting chimera (PROTAC), ribonuclease targeting chimera (RIBOTAC), targeted covalent inhibitors, topology-matching design and antiviral drug delivery system. This article is dedicated to Prof. Dr. Erik De Clercq, an internationally renowned expert in the antiviral drug research field, on the occasion of his 80th anniversary. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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34 pages, 9879 KiB

Open AccessReview

Advances and Perspectives in the Management of Varicella-Zoster Virus Infections

by Graciela Andrei and Robert Snoeck

Molecules 2021, 26(4), 1132; https://doi.org/10.3390/molecules26041132 - 20 Feb 2021

Cited by 61 | Viewed by 12699

Abstract

Varicella-zoster virus (VZV), a common and ubiquitous human-restricted pathogen, causes a primary infection (varicella or chickenpox) followed by establishment of latency in sensory ganglia. The virus can reactivate, causing herpes zoster (HZ, shingles) and leading to significant morbidity but rarely mortality, although in immunocompromised hosts, VZV can cause severe disseminated and occasionally fatal disease. We discuss VZV diseases and the decrease in their incidence due to the introduction of live-attenuated vaccines to prevent varicella or HZ. We also focus on acyclovir, valacyclovir, and famciclovir (FDA approved drugs to treat VZV infections), brivudine (used in some European countries) and amenamevir (a helicase-primase inhibitor, approved in Japan) that augur the beginning of a new era of anti-VZV therapy. Valnivudine hydrochloride (FV-100) and valomaciclovir stearate (in advanced stage of development) and several new molecules potentially good as anti-VZV candidates described during the last year are examined. We reflect on the role of antiviral agents in the treatment of VZV-associated diseases, as a large percentage of the at-risk population is not immunized, and on the limitations of currently FDA-approved anti-VZV drugs. Their low efficacy in controlling HZ pain and post-herpetic neuralgia development, and the need of multiple dosing regimens requiring daily dose adaptation for patients with renal failure urges the development of novel anti-VZV drugs. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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15 pages, 15160 KiB

Open AccessReview

Drug Discovery of Nucleos(t)ide Antiviral Agents: Dedicated to Prof. Dr. Erik De Clercq on Occasion of His 80th Birthday

by Guangdi Li, Tingting Yue, Pan Zhang, Weijie Gu, Ling-Jie Gao and Li Tan

Molecules 2021, 26(4), 923; https://doi.org/10.3390/molecules26040923 - 9 Feb 2021

Cited by 27 | Viewed by 6093

Abstract

Nucleoside and nucleotide analogues are essential antivirals in the treatment of infectious diseases such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), herpes simplex virus (HSV), varicella-zoster virus (VZV), and human cytomegalovirus (HCMV). To celebrate the 80th birthday of Prof. Dr. Erik De Clercq on 28 March 2021, this review provides an overview of his contributions to eight approved nucleos(t)ide drugs: (i) three adenosine nucleotide analogues, namely tenofovir disoproxil fumarate (Viread^®) and tenofovir alafenamide (Vemlidy^®) against HIV and HBV infections and adefovir dipivoxil (Hepsera^®) against HBV infections; (ii) two thymidine nucleoside analogues, namely brivudine (Zostex^®) against HSV-1 and VZV infections and stavudine (Zerit^®) against HIV infections; (iii) two guanosine analogues, namely valacyclovir (Valtrex^®, Zelitrex^®) against HSV and VZV and rabacfosadine (Tanovea^®-CA1) for the treatment of lymphoma in dogs; and (iv) one cytidine nucleotide analogue, namely cidofovir (Vistide^®) for the treatment of HCMV retinitis in AIDS patients. Although adefovir dipivoxil, stavudine, and cidofovir are virtually discontinued for clinical use, tenofovir disoproxil fumarate and tenofovir alafenamide remain the most important antivirals against HIV and HBV infections worldwide. Overall, the broad-spectrum antiviral potential of nucleos(t)ide analogues supports their development to treat or prevent current and emerging infectious diseases worldwide. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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15 pages, 1125 KiB

Open AccessReview

Development and Effects of Influenza Antiviral Drugs

by Hang Yin, Ning Jiang, Wenhao Shi, Xiaojuan Chi, Sairu Liu, Ji-Long Chen and Song Wang

Molecules 2021, 26(4), 810; https://doi.org/10.3390/molecules26040810 - 4 Feb 2021

Cited by 30 | Viewed by 6547

Abstract

Influenza virus is a highly contagious zoonotic respiratory disease that causes seasonal outbreaks each year and unpredictable pandemics occasionally with high morbidity and mortality rates, posing a great threat to public health worldwide. Besides the limited effect of vaccines, the problem is exacerbated by the lack of drugs with strong antiviral activity against all flu strains. Currently, there are two classes of antiviral drugs available that are chemosynthetic and approved against influenza A virus for prophylactic and therapeutic treatment, but the appearance of drug-resistant virus strains is a serious issue that strikes at the core of influenza control. There is therefore an urgent need to develop new antiviral drugs. Many reports have shown that the development of novel bioactive plant extracts and microbial extracts has significant advantages in influenza treatment. This paper comprehensively reviews the development and effects of chemosynthetic drugs, plant extracts, and microbial extracts with influenza antiviral activity, hoping to provide some references for novel antiviral drug design and promising alternative candidates for further anti-influenza drug development. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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13 pages, 1202 KiB

Open AccessReview

Advances in Antiviral Therapy for Subacute Sclerosing Panencephalitis

by Koichi Hashimoto and Mitsuaki Hosoya

Molecules 2021, 26(2), 427; https://doi.org/10.3390/molecules26020427 - 15 Jan 2021

Cited by 17 | Viewed by 5168

Abstract

Subacute sclerosing panencephalitis (SSPE) is a late-onset, intractable, and fatal viral disease caused by persistent infection of the central nervous system by a mutant strain of the measles virus. Ribavirin intracerebroventricular therapy has already been administered to several SSPE patients in Japan based on fundamental and clinical research findings from our group, with positive therapeutic effects reported in some patients. However, the efficacy of this treatment approach has not been unequivocally established. Hence, development of more effective therapeutic methods using new antiviral agents is urgently needed. This review describes the current status of SSPE treatment and research, highlighting promising approaches to the development of more effective therapeutic methods. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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Other

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6 pages, 749 KiB

Open AccessPerspective

Selected Thoughts on Hydrophobicity in Drug Design

by Lillian L. Lou and John C. Martin

Molecules 2021, 26(4), 875; https://doi.org/10.3390/molecules26040875 - 7 Feb 2021

Cited by 9 | Viewed by 2484

Abstract

The fundamental aim of drug design in research and development is to invent molecules with selective affinity towards desired disease-associated targets. At the atomic loci of binding surfaces, systematic structural variations can define affinities between drug candidates and biomolecules, and thereby guide the optimization of safety, efficacy and pharmacologic properties. Hydrophobic interaction between biomolecules and drugs is integral to binding affinity and specificity. Examples of antiviral drug discovery are discussed. Full article

(This article belongs to the Special Issue Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary)

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Successfully Fighting Viruses with Love for Chemistry: A Commemorative Issue in Honor of Prof. Dr. Erik De Clercq on the Occasion of His 80th Anniversary

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