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Matsuura K, Yamaura M, Sakawaki H, Himeno A, Pisil Y, Kobayakawa T, Tsuji K, Tamamura H, Matsushita S, Miura T. Sensitivity to a CD4 mimic of a consensus clone of monkey-adapted CCR5-tropic SHIV-MK38C. Virology 2023; 578:171-179. [PMID: 36580864 DOI: 10.1016/j.virol.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
By acclimatizing CCR5-tropic tier 1B SHIV-MK1 to rhesus monkeys, a tier 2 SHIV-MK38 strain with neutralization resistance and high replication ability was generated. In this study, we generated SHIV-MK38C, a monkey-infectious consensus molecular clone of SHIV-MK38. Analysis using pseudotype viruses showed that MK38C was tier 1C because it lacked the N169D mutation, which is the most important mutation for neutralization resistance. MK38C harboring the N169D mutation became tier 2. However, the replication ability of SHIV-MK38C with N169D was low; more than 17 weeks elapsed before its detection in monkeys. Tier 1C MK38C was sensitive to a CD4 mimic. Therefore, SHIV-MK38C could be used to evaluate CD4 mimics in vivo.
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Affiliation(s)
- Kanako Matsuura
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Mizuki Yamaura
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hiromi Sakawaki
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Ai Himeno
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yalcin Pisil
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Takuya Kobayakawa
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Kohei Tsuji
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Shuzo Matsushita
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Tomoyuki Miura
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.
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Kaku Y, Kuwata T, Gorny MK, Matsushita S. Prediction of Contact Residues in Anti-HIV Neutralizing Antibody by Deep Learning. Jpn J Infect Dis 2020; 73:235-241. [PMID: 32009060 DOI: 10.7883/yoken.jjid.2019.496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The monoclonal antibody 1C10 targets the V3 loop of HIV-1 and neutralizes a broad range of clade B viruses. However, the mode of interaction between 1C10 and the V3 loop remains unclear because crystallization of 1C10 and the V3 peptide was unsuccessful due to the flexible regions present in both 1C10 and the V3 peptide. In this study, we predicted the 1C10 amino acid residues that make contact with the V3 loop using a deep learning (DL)-based method. Inputs from ROSIE for docking simulation and FastContact, Naccess, and PDBtools, to approximate interactions were processed by Chainer for DL, and outputs were obtained as probabilities of contact residues. Using this DL algorithm, D95, D97, P100a, and D100b of CDRH3; D53, and D56 of CDRH2; and D61 of FR3 were highly ranked as contact residues of 1C10. Substitution of these residues with alanine significantly decreased the affinity of 1C10 to the V3 peptide. Moreover, the higher the rank of the residue, the more the binding activity diminished. This study demonstrates that the prediction of contact residues using a DL-based approach is a precise and useful tool for the analysis of antibody-antigen interactions.
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Affiliation(s)
- Yu Kaku
- Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University
| | - Takeo Kuwata
- Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University
| | | | - Shuzo Matsushita
- Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University
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