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Updated: Feb 4, 2026

Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro

Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro

Published on: September 26, 2025

SARS-CoV‑2メインプロテアーゼ阻害剤の抗ウイルスプロファイルに対する単一ハロゲン原子置換の影響

Haydar Bulut¹, Nobuyo Higashi-Kuwata², Hiromi Ogata-Aoki^2,3

¹Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, Maryland 20892, United States.

|February 2, 2026

Abstract:

The SARS-CoV-2 main protease (M^pro) remains a prime antiviral target because its inhibition halts viral replication. To probe how subtle atomic changes influence drug performance, we carried out a systematic halogen scan on a potent ketoamide scaffold, replacing a single fluorine with chlorine, bromine, or iodine. Enzymatic assays revealed that the F- and Cl-substituted analogues inhibit M^pro at nanomolar levels, whereas Br and I variants are 10- to 20-fold weaker. Cell-based antiviral tests mirrored this trend, yet uptake studies showed the opposite: iodine markedly enhances intracellular accumulation. High-resolution X-ray structures (1.6-1.8 Å) explain the dichotomy: small halogens fit snugly in the S1' σ-hole pocket, maximizing hydrogen-bond geometry, while bulkier atoms distort binding but create a lipophilic patch that boosts permeability. These data yield the first fluorine-to-iodine structure-activity map for SARS-CoV-2 M^pro inhibitors. These findings highlight the critical role of halogen selection in antiviral inhibitor design.

キーワード:

SARS-CoV-2 Mpro 阻害剤ハロゲン置換抗ウイルス薬構造活性相関薬物設計

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関連する概念動画

Halogens

Halogens

Group 17 elements, known as halogens, are nonmetals. At room temperature, fluorine and chlorine are gases, bromine is a liquid, and iodine a solid. Astatine is a highly unstable radioactive element, so currently, most of its properties are unknown due to its short half-life. Tennessine is a synthetic element also predicted to be in this group.

Diazonium Group Substitution with Halogens and Cyanide: Sandmeyer and Schiemann Reactions

Diazonium Group Substitution with Halogens and Cyanide: Sandmeyer and Schiemann Reactions

Arenediazonium substitution reactions occur when the diazonium group is substituted by various functional groups such as halides, hydroxyl, nitrile, etc. For instance, arenediazonium salts react with copper(I) salts of chloride, bromide, or cyanide to form corresponding aryl chlorides, bromides, and nitriles. These reactions are named Sandmeyer reactions. Although the mechanism of this reaction is complicated, as illustrated in Figure 1, they are believed to progress via an aryl copper...

Radical Substitution: Halogenation of Alkanes and Alkyl Substituents

Radical Substitution: Halogenation of Alkanes and Alkyl Substituents

In the presence of heat or light, alkanes react with molecular halogens to form alkyl halides by a substitution reaction called radical halogenation. This reaction has three steps: initiation, propagation, and termination, as seen in the radical chlorination of methane to produce methyl chloride.
In the initiation step of the reaction, the chlorine molecule undergoes homolytic cleavage in the presence of light or heat, forming two highly reactive chlorine radicals. Propagation occurs in two...

Atomic Structure

Atomic Structure

Atomic Mass

Atomic Mass

Atoms — and the protons, neutrons, and electrons that compose them — are extremely small. For example, a carbon atom weighs less than 2 × 10−23 g. When describing the properties of tiny objects such as atoms, we use appropriately small units of measure, such as the atomic mass unit (amu). The amu was originally defined based on hydrogen, the lightest element, then later in terms of oxygen. Since 1961, it has been defined with regard to the most abundant isotope of carbon, atoms of which...

Atomic Orbitals

Atomic Orbitals

An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.