diff --git a/pkgs/development/python-modules/mdtraj/default.nix b/pkgs/development/python-modules/mdtraj/default.nix
index 971688348a1d..a99b36c78765 100644
--- a/pkgs/development/python-modules/mdtraj/default.nix
+++ b/pkgs/development/python-modules/mdtraj/default.nix
@@ -11,6 +11,7 @@
 , wheel
 , astunparse
 , numpy
+, packaging
 , pyparsing
 , scipy
 , gsd
@@ -39,9 +40,31 @@ buildPythonPackage rec {
       url = "https://github.com/mdtraj/mdtraj/commit/81209d00817ab07cfc4668bf5ec88088d16904c0.patch";
       hash = "sha256-ttNmij7csxF0Z5wPPwhGumRX055W2IgFjRAe6nI6GNY=";
     })
+    # remove pkg_resources usage
+    # https://github.com/mdtraj/mdtraj/pull/1837
+    (fetchpatch {
+      name = "fix-runtime-error.patch";
+      url = "https://github.com/mdtraj/mdtraj/commit/02d44d4db7039fceb199c85b4f993244804f470d.patch";
+      hash = "sha256-nhbi3iOrDSM87DyIp1KVt383Vvb6aYOgkjuYzviqiq8=";
+    })
+    # remove distutils usage
+    # https://github.com/mdtraj/mdtraj/pull/1834
+    (fetchpatch {
+      name = "python312-compatibility.patch";
+      url = "https://github.com/mdtraj/mdtraj/commit/95d79747deef42c976ca362a57806b61933409f3.patch";
+      hash = "sha256-Cq7/d745q6ZgAyWGM4ULnSsWezsbnu1CjSz5eqYSb+g=";
+    })
+    # disable intrinsics when SIMD is not available
+    # TODO: enable SIMD with python3.12
+    # https://github.com/mdtraj/mdtraj/pull/1884
+    (fetchpatch {
+      name = "fix-intrinsics-flag.patch";
+      url = "https://github.com/mdtraj/mdtraj/commit/d6041c645d51898e2a09030633210213eec7d4c5.patch";
+      hash = "sha256-kcnlHMoA/exJzV8iQltH+LWXrvSk7gsUV+yWK6xn0jg=";
+     })
   ];
 
-  nativeBuildInputs = [
+  build-system = [
     cython_0
     oldest-supported-numpy
     setuptools
@@ -54,9 +77,10 @@ buildPythonPackage rec {
     llvmPackages.openmp
   ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     astunparse
     numpy
+    packaging
     pyparsing
     scipy
   ];
@@ -87,7 +111,9 @@ buildPythonPackage rec {
     "test_read_atomindices_2"
 
     # flaky test
+    "test_compare_rdf_t_master"
     "test_distances_t"
+    "test_precentered_2"
   ];
 
   pythonImportsCheck = [ "mdtraj" ];