AI-Driven De Novo Design and Molecular Modeling for Discovery of Small-Molecule Compounds as Potential Drug Candidates Targeting SARS-CoV-2 Main Protease.

Over the past three years, significant progress has been made in the development of novel promising drug candidates against COVID-19. However, SARS-CoV-2 mutations resulting in the emergence of new viral strains that can be resistant to the drugs used currently in the clinic necessitate the development of novel potent and broad therapeutic agents targeting different vulnerable spots of the viral proteins. In this study, two deep learning generative models were developed and used in combination with molecular modeling tools for de novo design of small molecule compounds that can inhibit the catalytic activity of SARS-CoV-2 main protease (Mpro), an enzyme critically important for mediating viral replication and transcription. As a result, the seven best scoring compounds that exhibited low values of binding free energy comparable with those calculated for two potent inhibitors of Mpro, via the same computational protocol, were selected as the most probable inhibitors of the enzyme catalytic site. In light of the data obtained, the identified compounds are assumed to present promising scaffolds for the development of new potent and broad-spectrum drugs inhibiting SARS-CoV-2 Mpro, an attractive therapeutic target for anti-COVID-19 agents.

A validated LC-MS/MS method for determination of six Anti-SARS-CoV-2 drugs in plasma and its application for a pharmacokinetic study in rats.

Antiviral treatment for COVID-19 is considered an effective tool in reducing the rate of severe cases and deaths. As of June 2023, a total of six small molecule antiviral drugs have been conditionally approved for marketing by the National Medical Products Administration (NMPA) within China. In this study, a method of HPLC-MS/MS was established and validated for the determination of six small molecule antiviral drugs in plasma using Lamivudine as an internal standard. The chromatographic separation was performed using gradient elution with an ACE 3 C18-PFP column (3.0 mm × 150 mm, 3 µm), and the mobile phase consisted of deionized water and acetonitrile/water (90:10, v/v), both with 10 mmol/L of ammonium acetate and 0.1 % ammonium hydroxide added. Quantitative analysis of the six small molecule drugs was carried out through selective reaction monitoring based on the positive ion spray ionization mode. The method exhibited excellent precision, accuracy, recovery, and linearity, and it was used to determine the pharmacokinetic characteristics in rats. Our work not only established a bioanalytical method for six small molecule antiviral drugs but also provided scientific references for clinical pharmacokinetic studies.

Study Protocol of a Randomized Controlled Clinical Trial to Evaluate the Efficacy and Safety of Ropeginterferon Alfa-2b in COVID-19 Patients with Comorbidities.

INTRODUCTION: Ropeginterferon alfa-2b represents a new-generation PEGylated interferon. It is approved for the treatment of polycythemia vera and shows promising anti-SARS-CoV-2 activities. OBJECTIVE: This clinical study aims to evaluate the efficacy and safety of ropeginterferon alfa-2b in patients with coronavirus disease 2019 (COVID-19) and comorbidities. METHODS: The randomized controlled study is designed to enroll adult patients with COVID-19 infection and comorbidities. Patients are non-responders to anti-SARS-CoV-2 drugs or not suitable to receive them. Comorbidities include hematologic cancer, solid tumor, and well-controlled autoimmune disease. Non-responders to anti-SARS-CoV-2 drugs are defined as having received treatment but have a Ct value < 30 at 14 days after symptom onset. Patients are randomized in a 1:1 ratio to receive ropeginterferon alfa-2b at 250 µg plus standard of care (SOC) or SOC alone. SARS-CoV-2 antigen test will be conducted at day 15 and day 29 visits to determine whether to administer additional ropeginterferon alfa-2b doses. Patients who are positive on the antigen test on days 15 and 29 will receive the second and third doses of ropeginterferon alfa-2b at 350 µg and 500 µg, respectively. Patients with a negative antigen test but a Ct value < 30 by reverse transcription polymerase chain reaction (RT-PCR) at days 15 and 29 are also administered the second (350 µg) and third (500 µg) doses. Patients at high risk of COVID-19 rebound/relapse, e.g., immunocompromised patients, will be given additional ropeginterferon alfa-2b doses even if the Ct is ≥ 30. Approximately 60 patients will be enrolled. PLANNED OUTCOMES: The primary outcome is to compare the time from randomization to the achievement of Ct value ≥ 30 by RT-PCR between ropeginterferon alfa-2b and control groups. Our previous studies have shown safety and promising anti-SARS-CoV-2 activities in patients with moderate or severe COVID-19. This study will provide valuable data in patients with COVID-19 and comorbidities, for whom safe and effective treatment is urgently needed. TRIAL REGISTRATION NUMBER: This trial is registered at ClinicalTrials.gov (Identifier NCT05808322).

A novel screening strategy of anti-SARS-CoV-2 drugs via blocking interaction between Spike RBD and ACE2.

Corona virus disease 2019 has spread worldwide, and appropriate drug design and screening activities are required to overcome the associated pandemic. Using computational simulation, blockade mechanism of SARS-CoV-2 spike receptor binding domain (S RBD) and human angiotensin converting enzyme 2 (hACE2) was clarified based on interactions between RBD and hesperidin. Interactions between anti-SARS-CoV-2 drugs and therapy were investigated based on the binding energy and druggability of the compounds, and they exhibited negative correlations; the compounds were classified into eight common types of structures with highest activity. An anti-SARS-CoV-2 drug screening strategy based on blocking S RBD/hACE2 binding was established according to the first key change (interactions between hesperidin and S RBD/hACE2) vs the second key change (interactions between anti-SARS-CoV-2 drugs and RBD/hACE2) trends. Our findings provide valuable information on the mechanism of RBD/hACE2 binding and on the associated screening strategies for anti-SARS-CoV-2 drugs based on blocking mechanisms of pockets.