Recently reported HIV-1 capsid (CA) inhibitors GS-CA1 and GS-6207 (an analog of GS-CA1) are first-in-class compounds with long-acting potential. Reportedly, both compounds have greater potency than currently approved anti-HIV drugs. Due to the limited access to experimental data and the compounds themselves, a detailed mechanism of their inhibition is yet to be delineated. Using crystal structures of capsid-hexamers bound to well-studied capsid inhibitor PF74 and molecular modeling, we predict that GS-CA compounds bind in the pocket that is shared by previously reported CA inhibitors and host factors. Additionally, comparative modeling suggests that GS-CA compounds have unique structural features contributing to interactions with capsid. To test their proposed binding mode, we also report the design of a cyclic peptide combining structural units from GS-CA compounds, host factors, and previously reported capsid inhibitors. This peptide (Pep-1) binds CA-hexamer with a docking score comparable to GS-CA compounds. Affinity determination by MicroScale thermophoresis (MST) assays showed that CA binds Pep-1 with a ~7-fold better affinity than well-studied capsid inhibitor PF74, suggesting that it can be developed as a possible CA inhibitor.

Coronaviruses (CoVs) are positive-stranded RNA viruses that infect humans and animals. Infection by CoVs such as HCoV-229E, -NL63, -OC43 and -HKU1 leads to the common cold, short lasting rhinitis, cough, sore throat and fever. However, CoVs such as Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and the newest SARS-CoV-2 (the causative agent of COVID-19) lead to severe and deadly diseases with mortality rates ranging between~1 to 35% depending on factors such as age and pre-existing conditions. Despite continuous global health threats to humans, there are no approved vaccines or drugs targeting human CoVs, and the recent outbreak of COVID-19 emphasizes an urgent need for therapeutic interventions. Using computational and bioinformatics tools, here we present the feasibility of reported broad-spectrum RNA polymerase inhibitors as anti-SARS-CoV-2 drugs targeting its main RNA polymerase, suggesting that investigational and approved nucleoside RNA polymerase inhibitors have potential as anti-SARS-CoV-2 drugs. However, we note that it is also possible for SARS-CoV-2 to evolve and acquire drug resistance mutations against these nucleoside inhibitors.Pathogens 2020, 9, 320 2 of 16 there were 2494 laboratory-confirmed cases of MERS, including 858 associated deaths, mostly from Middle East countries [9]. However, the current outbreak of SARS-CoV-2, the causative agent of Coronavirus Disease 2019 (COVID-19) has claimed thousands of lives since the first reported case in December, 2019, in Wuhan city, China [10][11][12]. To date, there are no approved vaccines or anti-SARS-CoV/MERS-CoV drugs available. Hence, studies on the discovery of small molecule drugs against SARS-CoV, MERS-CoV and other related future pathogenic coronaviruses are of high importance [13].CoVs belong to the family Coronaviridae of the Nidovirales order. CoVs have been divided into α, β, γ and δ-coronavirus genera [14]. The β CoVs have been further divided into four lineages (A-D) [15]. Phylogenic analysis shows that both SARS-CoV and SARS-CoV-2 belong to lineage B of β CoVs [16,17], whereas MERS-CoV belongs is lineage C, and the well-studied mouse hepatitis virus (MHV) in lineage A [18][19][20]. An example of lineage D is Rousettus bat coronavirus HKU9 [21]. Coronaviruses are the largest (26.2 to 31.7 kb) positive [or (+)] sense single stranded RNA viruses. The polyadenylated and capped RNA genome [5,22] has multiple open reading frames (ORFs). The 5 -most two-third of the genome contains ORF1a and ORF1b that encode polyproteins pp1a and pp1ab (made through a −1 ribosomal frameshift during translation), which are cleaved to form the non-structural proteins (nsp) [23][24][25][26][27][28][29][30]. The structural proteins are expressed as subgenomic RNAs and individual RNAs (genomic and subgenomic) are translated to yield only the protein encoded by the 5'-most ORF [31]. These polyproteins are processed by coronavirus-encoded papain-like proteinases (PL pro ; within nsp3) [32] and nsp5 (3C...

Coronaviruses (CoVs) are positive-stranded RNA viruses that infect humans and animals. Infection by CoVs such as HCoV-229E, -NL63, -OC43 and -HKUI1 leads to the common cold, short lasting rhinitis, cough, sore throat and fever. However, CoVs such as Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and the newest SARS-CoV-2 (the causative agent of COVID-19) lead to severe and deadly diseases with mortality rates ranging between ~1 to 35% depending on factors such as age and pre-existing conditions. Despite continuous global health threats to human, there are no approved vaccines or drugs targeting human CoVs, and the recent outbreak of COVID-19 emphasizes an urgent need for therapeutic interventions. Using computational and bioinformatics tools, here we present the feasibility of reported broad-spectrum RNA polymerase inhibitors as anti- SARS-CoV-2 drugs targeting its main RNA polymerase, suggesting that investigational and approved nucleoside RNA polymerase inhibitors have potential as anti-SARS-CoV-2 drugs. However, we note that it is also possible for SARS-CoV-2 to evolve and acquire drug resistance mutations against these nucleoside inhibitors.

The oligomerization of HIV-1 integrase onto DNA is not well understood. Here we show that HIV-1 integrase binds the DNA in a biphasic (high-and low-affinity) modes. For HIV-1 subtype B, the high-affinity mode is ~100-fold greater than low-affinity mode (K d.DNA =37 and 3400 nM, respectively). The Kd.DNA values of patient-derived integrases containing subtype-specific polymorphisms were affected 2-4-fold, suggesting that polymorphisms may influence on effective-concentrations of inhibitors, since these inhibitors preferably bind to integrase-DNA complex.

S56AptAmers gov: NCT02081625). The NS-065/NCNP-01 is a morpholino based antisense oligonucleotide that has been developed to skip the exon 53 of the dystrophin gene and to treat DMD patient amenable to the exon 53 skipping. It has been confirmed potent efficacy and high safety in pre-clinical studies. This clinical trial is an exploratory phase 1, single-site, first-in-human study. The primary endpoints are the safety and tolerability and the secondary endpoints are the pharmacokinetics and efficacies (dystrophin recovery). Three doses cohort design (1.25 mg/kg, 5 mg/kg and 20 mg/kg) was adopted and all subjects were dosed weekly intravenous infusion for 12 weeks. Mainly nonambulant subjects were recruited because the dose and duration in this trial was not enough to expect functional improvement. Of total 10 subjects, each three subjects were randomly assigned to 1.25 mg/ kg or 5 mg/kg cohorts, and four subjects were assigned to 20 mg/ kg cohort. An in vitro confirmation of dystrophin recovery and exon 53 skipping in subject-derived cells was one of inclusion criteria. Subject's mutations were classified into any of exons 45-52, 48-52 or 49-52 deletion; all NS-065/NCNP-01 treated cells satisfied the criteria. One week after an initial dosing for the first subject in each cohort, next subjects were dosed. Safety review committee advised the principal investigator whether or not to proceed to next cohort. At the end of 2014, dosing to all subjects had completed; no serious adverse events were observed. Dystrophin expression is to be evaluated by Western blotting and immunofluorescent staining. The analysis is still ongoing, but an immunofluorescent image analysis will be performed as objective and quantitative as possible by automated measurements. We would report progress of the first-in-human study of NS-065/ NCNP-01; the morpholino based exon 53 skipping drug for DMD.