Company: SMNR
Filing Date: 2025-08-13
Form Type: 424B3
Source: 0001193125-25-179226
Chunk: 936

Company: Semnur Pharmaceuticals, Inc.
Filing Date: 2025-08-13
Form: 424B3
Chunk 936
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 earlier delivery to each party of original, photocopied, or electronically transmitted signature pages that together
(but need not individually) bear the signatures of all other parties.

[The remainder of this page is intentionally left blank; signature pages to follow]

A-2-4

IN WITNESS WHEREOF the parties hereto have caused this Amendment to be duly executed as of the day and year first written above.

| DENALI CAPITAL ACQUISITION CORP. |     |                                 |
| By:                              |     | /s/ Lei Huang                   |
|                                  |     | Name: Lei Huang                 |
|                                  |     | Title:  Chief Executive Officer |
| DENALI MERGER SUB INC.           |     |                                 |
| By:                              |     | /s/ Peter Xu                    |
|                                  |     | Name: Peter Xu                  |
|                                  |     | Title:  President               |
| SEMNUR PHARMACEUTICALS, INC.     |     |                                 |
| By:                              |     | /s/ Jaisim Shah                 |
|                                  |     | Name: Jaisim Shah               |
|                                  |     | Title:  Chief Executive Officer |

A-2-5

Annex A-3

AMENDMENT NO. 2 TO AGREEMENT AND PLAN OF MERGER

THIS AMENDMENT NO. 2 TO AGREEMENT AND PLAN OF MERGER (this “”), dated as of July 22, 2025, is made and
entered into by and among Denali Capital Acquisition Corp., a Cayman Islands exempted company (which shall migrate to and domesticate as a Delaware corporation prior to the Closing, “”), Denali Merger Sub Inc., a Delaware
corporation and wholly owned subsidiary of Parent (the “” and together with Parent, collectively, the “”), and Semnur Pharmaceuticals, Inc., a Delaware corporation (the
“”).

WHEREAS, the Parent Parties and the Company have entered into an Agreement and Plan of Merger, dated as of
August 30, 2024 (as amended, restated, supplemented or otherwise modified from time to time, including pursuant to that certain Amendment No.1, dated as of April 16, 2025, the “”), providing for, among
other things, the merger of Merger Sub with and into the Company, with the Company continuing as the Surviving Corporation;

WHEREAS,
prior to the